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Interactive VISION reports for "KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
<p>This repository contains VISION reports for the KP-Tracer tumors described in the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al <em>bioRxiv</em> 2021).</p> <p>In this study, single-cell lineage tracing was performed in the <em>KP</em> autochthonous mouse model of non-small-cell lung cancer. Tumors were initiated with <em>Cre</em> recombinase (and optionally an additional gRNA targeting the other well-studied tumor suppressors) and allowed to grow for approximately 4-6 months at which point mice were sacrificed and tumors harvested. After purifying cancer cells by fluorescent markers, cells were profiled with the 10X chromium platform and four libraries were collected: a single-cell transcriptome library, a single-cell lineage tracing library, a single-cell multiplexing library, and a single-cell lenti-barcode library (used for confirming the clonality of tumors). Data was processed using the 10X Cellranger suite and custom pipelines as described in the manuscript above.</p> <p>For interactive work with these objects, users must first install VISION from Github (https://github.com/YosefLab/VISION) and then launch these reports either locally or on a server. For detailed instructions on how to launch reports, and create new reports for additional clones, please view our tutorials in our public reproducibility repository at https://github.com/mattjones315/KPTracer-release. </p>
Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
<p>This repository contains processed data associated with the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al <em>bioRxiv</em> 2021).</p> <p>In this study, single-cell lineage tracing was performed in the <em>KP</em> autochthonous mouse model of non-small-cell lung cancer. Tumors were initiated with <em>Cre</em> recombinase (and optionally an additional gRNA targeting the other well-studied tumor suppressors) and allowed to grow for approximately 4-6 months at which point mice were sacrificed and tumors harvested. After purifying cancer cells by fluorescent markers, cells were profiled with the 10X chromium platform and four libraries were collected: a single-cell transcriptome library, a single-cell lineage tracing library, a single-cell multiplexing library, and a single-cell lenti-barcode library (used for confirming the clonality of tumors). Data was processed using the 10X Cellranger suite and custom pipelines as described in the manuscript above. </p> <p>Data here represents the derived processed data from our analysis. The specific contents are described in a README contained within the repository.</p> <p>Briefly, however, we have provided here processed AnnData objects for the KP data (sgNT) and the integrated data across three genotypes (KP, KPA, and KPL). We also provide the gene lists associated with fitness, expansion annotations for each tree, as well as plasticity scores amongst other items. </p> <p>For code used in this study, we additionally have provided a reproducibility repository at https://github.com/mattjones315/KPTracer-release. </p>
Dataset from paper "Weathering of plastic SODIS containers and the impact of ageing on their lifetime and disinfection efficacy"
<ul> <li>Evolution of the molar mass distribution curves for the samples of both polypropylenes for each time of weathering.</li> <li>Evolution of the Differential Scanning Calorimetry (DSC) curves for the first melting for both polypropylenes.</li> </ul>
Adaptive and non-adaptive plasticity in changing environments: implications for sexual species with different life history strategies
<p>Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modelled as random noise and linear reaction norms that assume simple one-to-one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and non-adaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directional climate change. Non-adaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (i) smaller phenotypic than genotypic variance in the population (many-to-one genotype-phenotype map) and the coexistence of polymorphisms, and (ii) the maintenance of higher genetic variation – compared to linear reaction norms and genetic determinism – even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations producing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.</p>
Climate-induced plasticity in leaf traits of riparian plants
<p><strong>Aim:</strong> Leaf inputs from riparian vegetation and its decomposition play a key role in energy and nutrients transfer in many stream ecosystems. Instream leaf-litter decomposition is mainly driven by leaf traits. Therefore, understanding and predicting leaf traits variation with current environmental changes and its putative effects on stream food webs is a critical challenge. Most studies have focused on the assumed higher interspecific leaf traits variability, with little research addressing an intraspecific perspective.</p> <p><strong>Location:</strong> Andalusia, Spain</p> <p><strong>Methods:</strong> We assessed the relative effects of climate and soil on the intraspecific variability in leaf traits of four common woody riparian species in permanent low-order Mediterranean streams along a wide aridity gradient. We used a space-for-time substitution approach to predict leaf traits changes and consequences for stream food webs in a future climate change scenario.</p> <p><strong>Results:</strong> We found that climate had a major influence on intraspecific variability of leaf traits, but with opposite patterns depending on plant functional type. Results indicated that leaf quality—linked to palatability and decomposability—of Alnus glutinosa, Salix atrocinerea and Rubus ulmifolius (deciduous/semideciduous) will decrease with the forecasted aridification, whereas that of the evergreen Nerium oleander will increase.</p> <p><strong>Main conclusions:</strong> Our findings suggest a decrease of intraspecific leaf-quality in riparian deciduous species with global warming in a relatively short term, which, in a longer term, may add to the forecasted dieback of deciduous species in riparian corridors of temperate climate zones. These forecasted changes have the potential to significantly impair ecosystem functioning of Mediterranean mountain streams currently under deciduous gallery forests.</p>
Adaptive divergence generates distinct plastic responses in two closely related Senecio species
<p><span>The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variation they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (<i>Senecio, </i>Asteraceae). We sampled c.40 representative genotypes of each species from their native range on Mt Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little change in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is therefore associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.</span></p>
Thermal plasticity and evolution shape predator-prey interactions differently in clear and turbid water
<p>Warming and eutrophication negatively affect freshwater ecosystems by modifying trophic interactions and increasing water turbidity. We need to consider their joint effects on predator-prey interactions, and how these depend on the thermal evolution of both predator and prey.</p> <p>We quantified how 4°C warming and algae-induced turbidity (that integrates turbidity per se and increased food for zooplankton prey) affect functional response parameters and prey population parameters in a common-garden experiment. We did so for all combinations of high- and low-latitude predator (damselfly larvae) and prey (water fleas) populations to assess the potential impact of thermal evolution of predators and/or prey at a high latitude under warming using a space-for-time substitution. We then modelled effects on the system stability (i.e. tendency to oscillate) under different warming, turbidity and evolutionary scenarios.</p> <p>Warming and turbidity had little effect on the functional response parameters of high-latitude predators. In contrast, warming and turbidity reduced the handling times of low-latitude predators. Moreover, warming increased the search rates of low-latitude predators in clear water but instead decreased these in turbid water.</p> <p>Warming increased stability (i.e. prevented oscillations) in turbid water (except for the "high-latitude predator & high-latitude prey" system), mainly by decreasing the prey's carrying capacity and partly also by decreasing search rates, while it did not affect stability in clear water. Algae-induced turbidity generally decreased stability, mainly by increasing the prey's carrying capacity and partly also by increasing search rates. This resembles findings that nutrient enrichment can reduce the stability of trophic systems. The expected stability of the high-latitude trophic system under warming was dependent on the turbidity level: our results suggest that thermal plasticity tends to destabilize the high-latitude trophic system under warming in clear water but not in turbid water, and that thermal evolution of the predator will stabilize the high-latitude system under warming in turbid water but less so in clear water.</p> <p>The extent to which thermal plasticity and evolution shape trophic system stability under warming may strongly differ between clear and turbid water bodies, with their contributions having a more stabilizing role in turbid water.</p>
Unravelling processes between phenotypic plasticity and population dynamics in migratory birds
<p>Populations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking tactic in seasonal environments. However, the link between the population dynamics of migratory birds and migration tactic plasticity is not well understood.</p> <p>The quality of staging habitats affects individuals' migration timing and energy budgets in the course of migration, and can consequently affect individuals' breeding and overwintering performance, and impact population dynamics. Given staging habitats being lost in many parts of the world, our goal is to investigate responses of individual migration tactics and population dynamics in the face of loss of staging habitat, and to identify the key processes connecting them.</p> <p>We started by constructing and analysing a general full-annual-cycle individual-based model with a stylized migratory population to generate hypotheses on how changes in the size of staging habitat might drive changes in individual stopover duration and population dynamics. Next, through the interrogation of survey data, we tested these hypotheses by analysing population trends and stopover duration of migratory waterbirds experiencing loss of staging habitat.</p> <p>Our modelling exercise led to us posing the following hypotheses: the loss of staging habitat generates plasticity in migration tactics, with individuals remaining on the staging habitat for longer to obtain food due to a reduction in per capita food availability. The subsequent increasing population density on the staging habitat has knock on effects on population dynamics in the breeding and overwintering stage. Our empirical results were consistent with the modelling predictions.</p> <p>Our results demonstrate how environmental change that impacts one energetically costly life history stage in migratory birds can have population dynamics impacts across the entire annual cycle via phenotypic plasticity.</p>
Site fidelity and behavioral plasticity regulate an ungulate's response to extreme disturbance
<p>1. With rapid global change, the frequency and severity of extreme disturbance events are increasing worldwide. The ability of animal populations to survive these stochastic events depends on how individual animals respond to their altered environments, yet our understanding of the immediate and short-term responses of animals to acute disturbances remains poor.</p> <p>2. We focused on animal responses to the environmental disturbance created by megafire. Specifically, we explored the effects of the 2018 Mendocino Complex Fire in northern California, USA on the behaviour and body condition of black-tailed deer (<i>Odocoileus hemionus columbianus</i>). We predicted that deer would be displaced by the disturbance or experience high mortality post-fire if they stayed in the burn area.</p> <p>3. We used data from GPS collars on 18 individual deer to quantify patterns of home range use, movement, and habitat selection before and after the fire. We assessed changes in body condition using images from a camera trap grid. The fire burned through half of the study area, facilitating a comparison between deer in burned and unburned areas.</p> <p>4. Despite a dramatic reduction in vegetation in burned areas, deer showed high site fidelity to pre-fire home ranges, returning within hours of the fire. However, mean home range size doubled after the fire and corresponded with increased daily activity in a severely resource-depleted environment. Within their home ranges, deer also selected strongly for patches of surviving vegetation and woodland habitat, as these areas provided forage and cover in an otherwise desolate landscape. Deer body condition significantly decreased after the fire, likely as a result of a reduction in forage within their home ranges, but all collared deer survived for the duration of the study.</p> <p>5. Understanding the ways in which large mammals respond to disturbance like wildfire is increasingly important as the extent and severity of such events increases across the world. While many animals are adapted to disturbance regimes, species that exhibit high site fidelity or otherwise fixed behavioural strategies may struggle to cope with increased climate instability and associated extreme disturbance events.</p>
Rapid evolution of thermal tolerance and phenotypic plasticity in variable environments
<p>These are the data and code to go with "<strong>Rapid evolution of thermal tolerance and phenotypic plasticity in variable environments</strong>"</p> <p><strong>Figure 01 takes the following data/scripts:</strong></p> <p><a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20210610_Thally02_Figure01_plot_and_stats.R">20210610_Thally02_Figure01_plot_and_stats.R </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/track_keeper.csv">track_keeper.csv </a> and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/corr_Response%20growth%20.csv">corr_Response growth .csv </a>. These files contain growth rates per transfers for all selection environments throughout the experiment and growth rates in correlated environments during reciprocal transplants, respectively. </p> <p><strong>Figure 02 takes the following data/scripts:</strong></p> <p> </p> <p><a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20210610_Thally02_Figure02_plot_and_stats.R">20210610_Thally02_Figure02_plot_and_stats.R </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20161120_res_logis_t000.csv">20161120_res_logis_t000.csv </a>and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20161123_resloglint300.csv">20161123_resloglint300.csv .</a> These files contain the output of the shapes of the growth curves (i.e. information on lag time , growth at µmax, K etc) for all samples in all selection environments at t0 and t300, respectively</p> <p><strong>The remaining figures - position not clear at time of submission - take the following data/script. </strong></p> <p>For plasticity in FRRF data, the script 20181204_FRRF_plasticity.R takes the FRRF raw data contained in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/allfvfmdata_thally_t300_t000.csv">allfvfmdata_thally_t300_t000.csv </a>. Extracted parameters are in files <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/CvaluesThally02.csv">CvaluesThally02.csv</a>, <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/psiPSI_slope_intercept.csv">psiPSI_slope_intercept.csv</a>, and <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/rP_extracted_values.csv">rP_extracted_values.csv </a> and can be analysed using the R script <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/extracted%20parameter%20plots.R">extracted parameter plots.R .</a> R script <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/FRRF%20visualisation%20only%20.R">FRRF visualisation only .R </a> is for visualisation only, as the title suggests. </p> <p>For comparing plasticity/growth , the data are in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/20170327_giantbigtable.csv">20170327_giantbigtable.csv </a>, and can be visualised/analysed in <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/plast%20vs%20growth.R">plast vs growth.R </a></p> <p>In order to recreate the AMOVAS based on SNVs, use <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/all_variants_fixed-only_using_5x_depth_threshold.csv?versionId=01cbf6bf-fe16-4e7d-aae8-58c527596ebb">all_variants_fixed-only_using_5x_depth_threshold.cvs </a> with <a href="https://zenodo.org/api/files/cc14086e-84ed-4a13-b2d4-cf3cda0d669f/amova%20thally02.R?versionId=e9c21378-ee37-4418-9ce1-76db821e645a">amova thally02.R </a></p> <p>For additional information, please contact elisa.schaum@uni-hamburg.de </p>
Morphological integration, canalization, and plasticity in response to emergence time in Abutilon theophrasti
<p>The relationships between trait plasticity and canalization, and between phenotypic integration and plasticity, have been under debate, largely because direct evidence is still scarce for their associations, especially in response to environments. To investigate the relationships between canalization, integration and phenotypic plasticity in response to emergence time, we conducted a field experiment with an annual herbaceous species of <em>Abutilon theophrasti</em>, by subjecting plants to four treatments of emergence time (spring, late spring, summer and late summer), to measure a number of morphological traits and analyze correlations of plasticity with canalization and integration in these traits, at two stages of plant growth. Results showed plants with delayed emergence had higher phenotypic integration and more positive correlations between integration and plasticity, but less negative correlations between decreased canalization and plasticity, compared to those emerged in spring. Results suggested significant environmental changes that induce plastic responses, rather than environmental stress, can result in greater phenotypic integration in plants. Negative correlations between decreased canalization and plasticity occurred more frequently in plants emerging in spring and the least frequently in those emerging in summer, suggesting their relationship depends on specific environmental conditions and the degree of plasticity. Both increased phenotypic integration and decreased canalization might merely be the outcome of plastic responses, rather than mechanisms constraining or facilitating plasticity.</p>
Data and code from: Opposite, but insufficient, phenological responses to climate in two circumpolar seabirds: relative roles of phenotypic plasticity and selection
<p><span>The magnitude of climate change has been greatest in the Arctic, accelerating climate-induced shifts in phenology, but wildlife responses vary. Variation may be due to the relative importance of phenotypic plasticity or phenotypic selection.</span></p> <p><span>Here, we examine and contrast the environmental drivers of plasticity in breeding phenology of two circumpolar seabirds at their receding summer range limit using unique datasets of marked individuals </span><span>covering </span><span>25 and 30</span><span> years</span><span>. Based on prior knowledge of the local ecosystems, we predicted that climate would generate opposing patterns of plasticity in the two populations.</span></p> <p><span>Laying phenology of kittiwakes in the Gulf of Alaska was associated with a large-scale climate oscillation (Pacific Decadal Oscillation) while the Arctic-breeding murres adjusted </span><span>laying to sea-ice conditions. Kittiwakes laid earlier after experiencing colder climate about two years prior and laying dates did not advance over the study, but murres laid earlier when warmer climate led to earlier spring sea-ice break-up, and murre laying dates advanced by one week since 1990. Selection favoured earlier laying in both species.</span></p> <p><span>Both populations adjusted breeding phenology to environmental variation, but we anticipate opposing effects on phenology with continued climate change. Ice-constrained species can likely adapt to some extent because plasticity can provide the necessary shift to this physical barrier, although individuals were only able to adjust by ~one week while ice conditions advanced by over a month</span><span>. </span><span>In more temperate regions</span><span>,</span><span> where phenology is driven by bottom-up effects, plasticity and selection counteract one another leading to limited adaptability. We provide insights into the likely adjustments by Arctic marine animals to an increasingly warmer and ice-less summer.</span></p>
Plasticity in guarding superb starlings
<p class="MsoNormal">Cooperatively breeding vertebrates are common in unpredictable environments where the costs and benefits of providing offspring care fluctuate temporally. To balance these fitness outcomes, individuals of cooperatively breeding species often exhibit behavioral plasticity according to environmental conditions. Although individual variation in cooperative behaviors is well-studied, less is known about variation in plasticity of social behavior. Here, we examine the fitness benefits, plasticity, and repeatability of nest guarding behavior in cooperatively breeding superb starlings (<em>Lamprotornis superbus</em>). After demonstrating that the cumulative nest guarding performed at a nest by all breeders and helpers combined is a significant predictor of reproductive success, we model breeder and helper behavioral reaction norms to test the hypothesis that individuals invest more in guarding in favorable seasons with high rainfall. Variation in nest guarding behavior across seasons differed for individuals of different reproductive status: breeders showed plastic nest guarding behavior in response to rainfall, whereas helpers did not. Similarly, we found that individual breeders show repeatability and consistency in their nest guarding behavior while individual helpers did not. Thus, individuals with the potential to gain direct fitness benefits exhibit greater plasticity and individual-level repeatability in cooperative behavior.</p>
Data for: Individual differences in song plasticity in response to social stimuli and singing position
<p>Individual animals can react to the changes in their environment by exhibiting behaviours in an individual-specific way leading to individual differences in phenotypic plasticity. However, the effect of multiple environmental factors on multiple traits is rarely tested. Such a complex approach is necessary to assess the generality of plasticity and to understand how among-individual differences in the ability to adapt to changing environments evolve. This study examined whether individuals adjust different song traits to varying environmental conditions in the collared flycatcher (Ficedula albicollis), a passerine with complex song. We also aimed to reveal among-individual differences in behavioural responses by testing whether individual differences in plasticity were repeatable. The presence of general plasticity across traits and/or contexts was also tested. To assess plasticity, we documented 1) short-scale temporal changes in song traits in different social contexts (after exposition to male stimulus, female stimulus or without stimuli), and 2) changes concerning the height from where the bird sang (singing position), used as a proxy of predation risk and acoustic transmission conditions. We found population-level relationships between singing position and both song length and complexity, as well as social context-dependent temporal changes in song length and maximum frequency. We found among-individual differences in plasticity of song length and maximum frequency along both the temporal and positional gradients. These among-individual differences in plasticity were repeatable. Some of the plastic responses correlated across different song traits and environmental gradients. Overall, our results show that the plasticity of bird song 1) depends on the social context, 2) exists along different environmental gradients and 3) there is evidence for trade-offs between the responses of different traits to different environmental variables. Our results highlight the need to consider individual differences and to investigate multiple traits along multiple environmental axes when studying behavioural plasticity. </p>
Lack of avian predators is associated with behavioural plasticity in nest construction and height in an island songbird
<p>Orange-crowned warblers, Leiothlypis celata sordida, breeding on the California Channel Islands exhibit remarkable variation in their nest structure and placement, providing an intriguing exception to the general pattern that avian nest structure and nest site selection are highly conserved characters. We examined nest construction at both the population and individual scale to test whether warblers on Santa Catalina Island change their nest construction in response to nest height. At the population level, warblers built both lighter, grass-dominated ground nests and heavier off-ground nests that contained more ridged materials and less grass. The probability of nest success was significantly and positively correlated with nest height. At the individual level, we found the same individuals were capable of building on- and off-ground nests between nesting attempts within the same season. However, nest construction was highly variable among individuals and not significantly correlated with nest success after controlling for nest height. We suggest this observed behavioural plasticity in nest construction and nest height is a hierarchical response to the absence of avian predators. Reduced risk from avian predators appears to allow the warblers to use a variety of nest sites, thereby necessitating increased flexibility in nest construction.</p>
The phenotypic plasticity of an evolving digital organism
<p>Data set and R code used in the analysis reported in the manuscript entitled "<em>The phenotypic plasticity of an evolving digital organism</em>", which has been accepted in Proc. R. Open. Sci. for publication.</p>
Morphological plasticity in response to emergence time and population density in Abutilon theophrasti (Malvaceae)
<p>Increased density and delayed emergence are two major biotic factors in nature that have profound and complex effects on plants. No studies have attempt to compare the responses of plants to the two factors via morphological plasticity, particularly in dynamic patterns. We subjected plants of <em>Abutilon theophrasti</em> to four emergence times and three planting densities and measured and analyzed a number of mass and morphological traits at different growth stages. Across both stages, plants emerged in late spring had the highest total mass, and spring and late-spring plants had higher stem mass allocation than later germinants, but plants with delayed emergence had higher leaf and reproductive mass allocation, more leaves and less lateral roots, but lower stem length, stem and root diameter than early-emerged plants. Plants at high density performed lower in total mass and most other traits, but performed better in stem allocation and length, with shorter petioles and lateral roots, than at lower densities. In competition for resources, plants will prefer stem elongation to leaf/root growth, and even at the cost of reproduction to ensure the survival of the present generations when competition is intense or lethal. By contrast, plants will prefer the investment into leaf and reproductive growth to stem/root growth, for offspring persistence, when shortened lifetime does not threaten the contemporary survival. The contrasting strategies revealed the intelligence of plants in balancing between survival, growth and reproduction, depending on environmental contexts.</p>
Data from: Lineage-specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago.
<p><span>Two asexual lineages, JPN1 and JPN2, of panarctic <em>Daphnia pulex</em> expanded the distribution range to Japan from North America, independent of each other. According to the mutation rates within these lineages, JPN1 lineage colonized Japan earlier than JPN2 lineage. Moreover, the ratio of nonsynonymous to synonymous mutation rates (dN/dS) was lower in JPN1 than in JPN2 lineage.</span></p> <p><span>Accordingly, it is hypothesized that variations of phenotypic traits differ between these two lineages. In addition, since they are obligate parthenogenetic animals, the lineage occupying a larger distribution range should have a larger phenotypic plasticity. To test these hypotheses, we experimentally examined the phenotypic variations of fitness-related traits, including digestive, life history and morphological traits, among several genotypes of these lineages.</span></p> <p><span>We found that within-lineage variations of most traits were smaller in JPN1 than in JPN2. In addition, the overall phenotypic variations were also smaller within the JPN1 lineage than within the JPN2 lineage. These results support the idea that the JPN1 lineage has been more efficiently subjected to negative selection, as expected from the lower dN/dS ratio.</span></p> <p><span>However, the magnitude of the phenotypic plasticity to changing food levels was at the same level for both the JPN1 and JPN2 lineages, while variations found in the phenotypic plasticity were smaller in the JPN1 lineage. The difference in the variations of the phenotypic traits and plasticity between the two lineages suggests that these two lineages have evolved under somewhat different environmental conditions and that genotypes of the JPN2 lineage may have exploited niches that differed somewhat from that of the JPN1 genotypes.</span></p>
Maximization of fitness by phenological and phenotypic plasticity in range expanding rabbitfish (Siganidae)
<p>Global warming is modifying the phenology, life-history traits and biogeography of species around the world. Evidence of these effects have increased over recent decades; however, we still have a poor understanding of the possible outcomes of their interplay across global climatic gradients, hindering our ability to accurately predict the consequences of climate change in populations and ecosystems. We examined the effect that changes in biogeography can have on the life-history traits of two of the most successful range-extending fish species in the world: the tropical rabbitfishes Siganus fuscescens and Siganus rivulatus. Both species have established abundant populations at higher latitudes (poleward) in the northern and southern hemispheres and have been identified as important ecological engineers with the potential to alter the community structure of seaweed forests (Laminariales and Fucales) in temperate regions. Life-history trait information from across their global distribution was compiled from the published literature and meta-analyses were conducted to assess changes in (i) the onset and duration of reproductive periods, (ii) fecundity, (iii) size at maturity, (iv) growth rates, (v) maximum body sizes and (vi) longevity in populations at the leading edge of range expansion in relation to sea surface temperature and primary productivity (i.e., a common proxy for nutritional resource levels). Populations at highest latitudes had shortened their reproductive periods and reduced growth rates, taking longer to reach sexual maturity and maximum sizes, but compensated this with higher fecundity per length class and longer lifespans than populations in warmer environments. Low primary productivity and temperature in the Mediterranean Sea resulted in lower growth rates and body sizes for S. rivulatus, but also lower length at maturity, leading to increased life-time reproductive output. The results suggest that plasticity in the phenology and life-history traits of range-expanding species would be important to enhance their fitness in high latitude environments, facilitating their persistence and possible further poleward expansions. Quantifying the magnitude and direction of these responses can improve our understanding and ability to forecast species redistributions and its repercussions in the functioning of temperate ecosystems. </p>
Provenance rather than nitrogen addition dominate the phenotypes and plasticity of Ambrosia artemisiifolia in China
<p><span>Phenotypic plasticity, which differs between species, populations, individuals, even traits, is considered as one of the mechanisms of plant invasion. We conducted a common garden experiment with six provenances (HRB, CC, HG, ML, MZ, LB) of <em>Ambrosia artemisiifolia</em> and three nitrogen addition treatments to test their performance response. In order to explore the adaptation strategies of <em>A. artemisiifolia </em>towards heterogeneous habitats, phenotypic plasticity indexes were calculated to analyze among different provenances and traits. All traits were significantly influenced (<em>P</em><0.05) by provenance, except for number of inflorescences, inflorescences length and intercellular CO<sub>2</sub> concentration. Nitrogen addition notably affected on seed length, root biomass ratio, root-shoot ratio and four physiological traits (Pn, Tr, Gs, Ci). Among six provenances, the phenotypic plasticity index differed significantly (<em>P</em><0.05), but there were no significant differences of plasticity among nitrogen treatments. And biomass phenotypic plasticity was relatively higher both in response to prevenance and to nitrogen. We also found that only the plasticity of 100-seed weight was closely related to latitude, climate and genetic factors. In summary, provenances had a greater impact on the phenotype and plasticity of <em>A. artemisiifolia</em> than nitrogen addition, indicating the potential for further evolution of plasticity. Differences in plasticity among provenances and traits are important in predicting the invasion trend of <em>A. artemisiifolia</em> in the future.</span></p>
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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.