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77 results for “transplant experiment”
Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change
<p>Recent climatic changes, such as more frequent droughts and heatwaves, can lead to rapid evolutionary adaptations in plant populations. Such rapid evolution can be investigated using the resurrection approach by comparing plants raised from stored ancestral and contemporary seeds from the same population. This approach has so far only been used in common garden experiments, allowing it to reveal genetic differentiation but not adaptation. In this study, we performed a novel approach by testing for evolutionary adaptation in natural plant populations using a resurrection study in combination with in situ transplantations. We cultivated seedlings from ancestors (23–26 years old) and contemporary descendants of three perennial species (<em>Melica ciliata, Leontodon hispidus</em> and <em>Clinopodium vulgare</em>) from calcareous grasslands in the greenhouse and transplanted them back to their collection sites. In addition, we sowed seeds of ancestors and descendants of two species (<em>L. hispidus</em> and <em>C. vulgare</em>) to the collection sites in order to investigate germination rates. In transplanted <em>M. ciliata</em> seedlings, we observed lower mortality and larger plant size in descendants compared to ancestors. This indicates that descendants are better adapted than ancestors to the current environmental conditions, which proved to be exceptionally hot and dry during the study period. Descendants of <em>C. vulgare</em> seedlings tended to be smaller and descendants of <em>L. hispidus</em> seedlings produced fewer leaves compared to their ancestors in their contemporary environmental conditions. In <em>C. vulgare</em> and <em>L. hispidus</em>, we found evolution towards faster germination, and especially descendant seeds of <em>C. vulgare</em> were better adapted to the unfavourable conditions during the experimental period. Concluding, we demonstrate that our novel approach to combine resurrection ecology with transplant experiments is a promising avenue to rigorously test for evolutionary adaptations in changing environments.</p>
Raw Data for the article: Liver transplantation for unresectable intrahepatic cholangiocarcinoma: an Italian experience
<p>Intrahepatic cholangiocarcinoma (iCCA) is an aggressive form of primary liver cancer treated exclusively with surgery.</p> <p>Its incidence in the western world is growing lately [<a href="https://link.springer.com/article/10.1007/s13304-021-01064-w#ref-CR1">1</a>] and the overall 5-year survival is poor due to late diagnosis, since patients rarely present a jaundice differently from patients affected by perihilar cholangiocarcinoma. Ideally liver resection and regional lymphadenectomy are the best treatments; however, these are unfortunately connotated by a 75% recurrence rate 5 years after surgery. Systemic chemotherapy offers a minimal response, as well as loco-regional therapy such as selective internal radiotherapy (SIRT), with a survival varying from 11 to 15 months between the two therapies</p>
Data from: Cedrus libani survival and growth data from a transplant experiment and natural forests in northern Lebanon
<p><strong>Aims</strong></p> <p>The <em>Cedrus</em> dataset was set up to assess the climatic niche breadth of <em>Cedrus libani –</em> a relict mountain species <em>–</em> by comparing field observations and transplant experiment measurements within and beyond the elevational range limits of <em>Cedrus</em> under natural conditions.</p> <p><strong>Location</strong></p> <p>Lebanon - Near East - Mediterranean region</p> <p><strong>Methods</strong></p> <p>The transplant experiment included 8 common gardens at altitudes ranging from 110 to 2330 m, within and far beyond the warm and cold limits of Cedar distribution under natural conditions. It was set up in 2018, and monitored for three years until fall 2021 to study survival and growth of the Cedar of Lebanon (<em>Cedrus libani</em>) and 3 potentially competing species (<em>Quercus calliprinos, Quercus infectoria and </em><em>Pinus</em> <em>brutia</em>). Field observations of Cedar presence/absence were carried out on 1023 sites.</p> <p><strong>Results</strong></p> <p>We observed surprisingly high survival and growth rates of Cedar at elevations well below its natural range in Lebanon. Below its elevational limit of 1300 m under natural conditions, water stress limited the survival of juvenile Cedars at elevations below 500 m, and its low competitiveness below 900 m explained its absence between 500 and 900 m elevation. On the other hand, cold temperature and water stress limited its survival at elevations slightly above the observed natural upper elevational limit of 1830 m.</p> <p><strong>Main conclusions</strong></p> <p>The experimental setup demonstrated that the elevational range suitable for the growth and survival of the Cedar of Lebanon is twice as large as the range within which Cedar is observed today under natural conditions. The high survival rate beyond the lower limit of its natural range raises hope for its resilience to ongoing climate warming. If this pattern were common to other mountain species, it would challenge predictions of massive extinction linked to climate change, and pave the way for promoting adaptive actions such as competition management to improve their survival.</p>
Data for: Testing for fitness epistasis in a transplant experiment identifies a candidate adaptive locus in Timema stick insects
<p>Identifying the genetic basis of adaptation is a central goal of evolutionary biology. However, identifying genes and mutations affecting fitness remains challenging because a large number of traits and variants can influence fitness. Selected phenotypes can also be difficult to know <em>a priori</em>, complicating top-down genetic approaches for trait mapping that involve crosses or genome-wide association studies. In such cases, experimental genetic approaches, where one maps fitness directly and attempts to infer the traits involved afterward, can be valuable. Here, we re-analyse data from a transplant experiment involving <em>Timema</em> stick insects, where five physically clustered SNPs associated with cryptic body colouration were shown to interact to affect survival. Our analysis covers a larger genomic region than past work and revealed a locus previously not identified as associated with survival. This locus resides near a gene, <em>Punch</em> (<em>Pu</em>), involved in pteridine pigments production, implying that it could be associated with an unmeasured colouration trait. However, by combining previous and newly obtained phenotypic data, we show that this trait is not eye or body colouration. We discuss the implications of our results for the discovery of traits, genes, and mutations associated with fitness in other systems, as well as for supergene evolution.</p>
Methods of species pool determination as predictors of survival in seeding and transplanting experiments
<ol> <li><span>Community composition is limited by a species' ability to reach, establish, and survive on a site. Establishment and survival are constrained by both abiotic conditions and biotic interactions that operate together on local scales. They decide which species from the pool will form the community. For this reason, it is very important to clearly define the species pool, against which the community composition is compared. </span></li> <li><span>The effect of biotic and abiotic factors can be assessed experimentally, and the species pool by using estimation methods based on broad-scale observational data. We compared success of five species pool estimation methods in predicting establishment and survival in a seed/transplant addition experiment. </span></li> <li> <span>In four different locations, we added resident and non-resident species to plots with and without competition and</span><span> tested the ability of the species to thrive in both competition-free gaps (constrained mainly by abiotic conditions) and in intact vegetation (complete community filter). In these treatments, we studied the seedling recruitment and survival, and the establishment and survival of pre-grown transplants. The ability of species pool assessment methods to predict species performance in individual treatments was compared. The comparison of results from individual treatments indicates the importance of individual components of the community filter. </span> </li> <li><span>Species pool assessment methods, based on species co-occurrence patterns (Beals index, Favourability, and Unconstrained ordination), were the best predictors of species performance in the intact vegetation but were less successful in the competition-free environment. Methods based on co-occurrence patterns were the most effective for predicting seedling establishment, while seed germination alone and transplant survival were poorly predictable. </span></li> <li><span>The biotic filter was the principal factor defining our community composition, especially for the process of seedling establishment. The roles of biotic and abiotic filters are very difficult to distinguish without an experimental approach and the ratio of their importance changes during plant ontogenesis.</span></li> </ol>
Data from: Differences between two populations of <em>Stipa krylovii</em> in adaptive strategies: analysis of a three-year reciprocal transplant experiment
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Data from: Reassessing adaptational lag in <em>Eriophorum vaginatum</em>: Short-term responses to reciprocal transplant and passive warming experiments in northern Alaska
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Data from: Climate limitation at the cold edge – contrasting perspectives from species distribution modelling and a transplant experiment
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Data for: Testing for fitness epistasis in a transplant experiment identifies a candidate adaptive locus in Timema stick insects
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Phenotypic, fitness and environmental data in support of the publication: selection favors adaptive plasticity in a long-term reciprocal transplant experiment
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Cedrus libani survival and growth data from a transplant experiment and natural forests in northern Lebanon
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Methods of species pool determination as predictors of survival in seeding and transplanting experiments
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Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change
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Disentangling the effects of methanogen community and environment on peatland greenhouse gas production by a reciprocal transplant experiment
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Effect of calcium addition on litter decomposition; data from reciprocal litter transplant experiment at Hubbard Brook, NH
Cross-site syntheses of litter decomposition studies have shown that litter calcium (Ca) concentration may have a role in controlling the extent of decomposition of tree foliage. We used an ongoing watershed CaSiO4 addition experiment at the Hubbard Brook Experimental Forest in New Hampshire, USA, to test the hypotheses that increased Ca in litter would have no effect on the initial rates of litter decay but would increase the extent or completeness (limit value) of foliar litter decomposition. We tested these hypotheses with a 6-year litter decomposition experiment using foliar litter of four tree species that are prominent at this site and in the Northern Hardwood forest type of North America: sugar maple (Acer saccharum Marsh), American beech (Fagus grandifolia Ehrh.) yellow birch (Betula alleghaniensis Britt.) and white ash (Fraxinus americana L.). The experiment used a reciprocal transplant design with the Ca-treated watershed and a control site providing two sources of litter and two placement sites. This dataset includes mass loss and changes in nutrient content of litter over the six year period.
Data from: Measuring microbial fitness in a field reciprocal transplant experiment
Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments.
Data from: Modeling intraspecific adaptation of Abies sachalinensis to local altitude and responses to global warming, based on a 36-year reciprocal transplant experiment
Intraspecific adaptation in Abies sachalinensis was examined using models based on long-term monitoring data gathered during a reciprocal transplant experiment with eight seed source populations and six transplantation sites along an altitudinal gradient. The consequence of local adaptation was evaluated by testing the home-site advantage for upslope and downslope transplants at five ages. The populations' fitness-linked trait was set as their productivity (tree height ×survival rate) at each age. The effects of global warming were evaluated on the basis of the 36-year performance of downslope transplants. Evidence was found for adaptive genetic variation affecting both height and survival from an early age. Increasing the distance between seed source and planting site significantly reduced productivity for both upslope and downslope transplantation, demonstrating the existence of a significant home-site advantage. The decrease in productivity was most distinct for upslope transplantations, indicating strong local adaptation to high altitudes. Global warming is predicted to increase the productivity of high-altitude populations. However, due to their existing local adaptation, all tested populations exhibited lower productivity under warming than demes that were optimal for the new climate. These negative predictions should be considered when planning the management of locally-adapted plant species such as A. sachalinensis.
Data from: Variation of xylem vessel diameters across a climate gradient: insight from a reciprocal transplant experiment with a widespread boreal tree
Xylem vessel diameters represent an important plant hydraulic trait to ensure sufficient water supply from the roots to the leaves. The ability to adjust the hydraulic pathway to environmental cues is key in order to satisfy transpirational demands and maximize growth and survival. We evaluated the variability of vessel diameters in trembling aspen in a reciprocal transplant experiment. We tested six provenances from three ecological regions of North America planted at four test sites in western Canada. All test sites were established at the same time with the same provenances arranged in a randomized complete block design. Vessel diameter showed a strong interaction of population and test site suggesting a high degree of phenotypic plasticity in this trait. Gaussian kernel density estimates support plastic as well as genetic contributions in vessel diameter control trending from bimodal distributions at the most northern test site towards unimodal distributions at the warmest and mildest test site. Furthermore, we used test site-specific climate data in form of a 2-year, 5-year and 10-year average of 21 directly and derived climatic variables and found that average site-specific vessel diameters correlated strongly with summer moisture availability. A previously found negative relationship with vessel diameter and tree height in central Alberta was also found at two other boreal test sites but reversed at a wetter and milder sub-boreal test site. In summary, vessel diameters were highly plastic in response to different environments and varied with summer moisture availability. The variability of vessel diameter and tree height correlations suggests that vessel diameter alone cannot serve as a reliable proxy for long-term growth performance beyond boreal environments. Instead, selecting aspen populations with a high degree of plasticity in this trait appears to be the safest option for assisted migration and seed transfer programmes under climate change.
Data from: The response of the alpine dwarf shrub Salix herbacea to altered snowmelt timing: lessons from a multi-site transplant experiment
Climate change is altering spring snowmelt patterns in alpine and arctic ecosystems, and these changes may alter plant phenology, growth and reproduction. To predict how alpine plants respond to shifts in snowmelt timing, we need to understand trait plasticity, its effects on growth and reproduction, and the degree to which plants experience a home-site advantage. We tested how the common, long-lived dwarf shrub Salix herbacea responded to changing spring snowmelt time by reciprocally transplanting turfs of S. herbacea between early-exposure ridge and late-exposure snowbed microhabitats. After the transplant, we monitored phenological, morphological and fitness traits, as well as leaf damage, during two growing seasons. Salix herbacea leafed out earlier, but had a longer development time and produced smaller leaves on ridges relative to snowbeds. Longer phenological development times and smaller leaves were associated with reduced sexual reproduction on ridges. On snowbeds, larger leaves and intermediate development times were associated with increased clonal reproduction. Clonal and sexual reproduction showed no response to altered snowmelt time. We found no home-site advantage in terms of sexual and clonal reproduction. Leaf damage probability depended on snowmelt and thus exposure period, but had no short-term effect on fitness traits. We conclude that the studied populations of S. herbacea can respond to shifts in snowmelt by plastic changes in phenology and leaf size, while maintaining levels of clonal and sexual reproduction. The lack of a home-site advantage suggests that S. herbacea may not be adapted to different microhabitats. The studied populations are thus unlikely to react to climate change by rapid adaptation, but their responses will also not be constrained by small-scale local adaptation. In the short term, snowbed plants may persist due to high stem densities. However, in the long term, reduction in leaf size and flowering, a longer phenological development time and increased exposure to damage may decrease overall performance of S. herbacea under earlier snowmelt.
Data from: A new approach to study local adaptation in long-lived organisms: virtual transplant experiments
1. Despite the importance of local adaptation and the extended literature that has addressed it, there are few methods available to explore local adaptation across large temporal scales. However, long-term patterns are likely to be essential to understanding adaptation in long-lived species, such as trees. 2. Here, we propose a methodology named 'virtual transplant experiment' (VTE), which uses long-term climatic variability to explore local adaptation to climate in natural tree populations. VTEs evaluate the historical response of populations to their local climate and to climates representative of conditions in other populations. We tested our methodology using simulated data and applied it in two case studies on: (i) Pinus nigra populations at the edge of the species distribution, where previous research has suggested strong climate adaptation, and (ii) Fagus sylvatica mesic populations, where parallel experiments showed no adaptation to macroclimate. 3. VTE results from simulated and real-world data matched our expectations, suggesting that the method accurately identified the patterns of local adaptation to climate in tree populations. VTEs consistently discriminated locally adapted populations in synthetic data with a known degree of local adaptation. As expected, P. nigra populations showed adaptation to local climate in the VTE, while F. sylvatica populations showed no overall local advantage. 4. Our method provides a new way to test for local adaptation over time scales encompassing the complete lifespan of trees. VTEs can complement current methods to study local adaptation by adding the ability to explore the long-term response to local climate in natural populations. The advantages and limitations of the different approaches to studying local adaptation stress the importance of combining multiple approaches to test for local adaptation in long-lived organisms.
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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.
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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.