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1,363 results for “phenotypic data”
Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
<p>A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiont <em>Sinorhizobium meliloti</em> paired with two genotypes of the host <em>Medicago truncatula</em> in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype – partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments.</p> <p><span>IMPORTANCE:</span><strong> </strong>Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.</p>
Data from: The phenotypic determinants of diet variation between divergent lineages of threespine stickleback
<p><span>Lineages with independent evolutionary histories often differ in both their morphology and</span> <span>diet. Experimental work has improved our understanding of the links between the biomechanics of morphological traits and foraging performance (trait-utility). However, because the expression of foraging-relevant traits and their utility can be highly context-specific, it is often unclear how dietary divergence arises from evolved phenotypic differences. Here, we explore the phenotypic causes of dietary divergence between two genetically and phenotypically divergent lineages of threespine stickleback (Gasterosteus aculeatus) with independent evolutionary histories of freshwater colonization and adaptation. First, using individuals from a line-cross breeding design, we conducted 150 common-garden foraging trials with a community of multiple prey species and performed morphological and behavioural analyses to test for prey-specific trait-utility. Second, we tested if the traits that explain variation in foraging performance among all individuals could also explain the dietary divergence between the lineages. Overall, we found evidence for the utility of several foraging traits, but these traits did not explain the observed dietary divergence between the lineages in common garden. This work suggests that evolved dietary divergence results not only from differences in morphology but also from divergence in behaviours that underlie prey capture success in species-rich prey communities.</span></p>
Data from: Disentangling genetic from environmental effects on phenotypic variability of Southern rock lobster (Jasus edwardsii) postlarvae
<p><span>Environmental conditions experienced during larval dispersal of marine organisms can determine size-at-settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here we investigated morphological differences in recently settled southern rock lobster (<em>Jasus</em> <em>edwardsii</em>) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction-site associated DNA sequencing (ddRADseq) to assess differences in genetic structure of recently settled recruits on the east coast of Tasmania over three months of peak settlement during 2012 (August, September and October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller individuals found at the northernmost site. Also, there was a lack of overall genetic divergence; however, significant differences in pairwise FST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, individuals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic divergence in the presence of phenotypic variation indicates that larval environmental history during dispersal of <em>J</em>. <em>edwardsii</em> could be a possible driver of the resulting phenotype of settlers.</span></p>
Data for: Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback
<p>Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here 'parallel evolution') often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (<em>Gasterosteus aculeatus</em>) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.</p>
Phenotypic and ecological data from: Widespread convergent morphological evolution within the largest family of songbirds
<p>Although convergence is a common evolutionary phenomenon, few studies have quantified its prevalence across a large, densely sampled clade. Large-scale phylogenies and the advent of novel computational methods facilitate more robust identification of convergent events and their statistical significance. The tanagers (Aves: Thraupidae), the largest family of songbirds, offer an excellent opportunity to study the extent of phenotypic convergence in response to similar ecological pressures on a continental scale. To investigate convergence in the group, we used the largest phylogenetic and multivariate morphological dataset to date for the clade. First, we used phylogenetic comparative analyses to show a correlation between diet and aspects of bill shape. We then investigated our dataset for the presence and magnitude of convergent events and assessed significance through simulations and modeling analyses. Overall, we found that around half (45.3%) of species and clades we tested have converged in morphological space more than would be expected by chance alone. Our study shows that across Thraupidae, various bill shapes have evolved convergently to fill multiple distinct sections of ecological niche space, reflecting a signal of ecological opportunity and structural constraints.</p>
Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation
<p>Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus <em>Ehrharta, </em>whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of <em>Ehrharta </em>and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualises multiple values of K. Given that the two genomic data sets are fully independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the <em>E. setacea</em> and <em>E. rehmannii </em>complexes, with the <em>E. ramosa</em> complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach.</p>
Data for: Phenotypic plasticity increases exposure to extreme climatic events that reduce individual fitness
<p>Climate models, and empirical observations, suggest that anthropogenic climate change is leading to changes in the occurrence and severity of extreme climatic events (ECEs). Effects of changes in mean climate on phenology, movement, and demography in animal and plant populations are well documented. In contrast, work exploring the impacts of ECEs on natural populations is less common, at least partially due to the challenges of obtaining sufficient data to study such rare events. Here, we assess the effect of changes in ECE patterns in a long-term study of great tits, near Oxford, over a 56-year period between 1965 and 2020. We document marked changes in the frequency of temperature ECEs, with cold ECEs being twice as frequent in the 1960s than at present, and hot ECEs being ~three times more frequent between 2010 and 2020 than in the 1960s. While the effect of single ECEs was generally quite small, we show that increased exposure to ECEs often reduces reproductive output, and that in some cases, the effect of different types of ECE is synergistic. We further show that long-term temporal changes in phenology, resulting from phenotypic plasticity, lead to an elevated risk of exposure to low-temperature ECEs early in reproduction, and hence suggest that changes in ECE exposure may act as a cost of plasticity. Overall, our analyses reveal a complex set of risks of exposure and effects as ECE patterns change and highlight the importance of considering responses to changes in both mean climate and extreme events. Patterns in exposure and effects of ECEs on natural populations remain underexplored and continued work will be vital to establish the impacts of ECEs on populations in a changing climate.</p>
Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses
<p>Switchgrass (<em>Panicum virgatum</em> L.) is a model herbaceous bioenergy crop in the USA. It is a native, perennial, warm-season grass, and has broad adaptability. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Significant genetic variation for biomass yield observed in lowland switchgrass hybrids. Due to the quantitative inheritance of biomass yield, varietal improvement for the trait through conventional breeding is slow. Therefore, quantitative trait loci (QTL) mapping is used to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped seven biparental crosses and one combined cross of two biparental crosses (30 to 96 F1s) between lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass yield, plant height, and clonal mass scores in a simulated-sward plot with two replications at two locations in Tennessee from 2019 to 2021. The crosses were genotyped using 17,251 single nucleotide polymorphisms generated through genotyping-by-sequencing. QTL mapping was performed using a single-QTL model in R-QTL. The study identified major QTL for biomass yield, plant height, and clonal mass scores resided on chromosomes 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively.</p> <p>The dataset contains five files describing the phenotype and genotype of each individual used in the quantitative trait loci (QTL) analysis.</p> <ul> <li>'File 1' contains biomass yield, plant height, and clonal mass data for each genotype and parents evaluated at two locations in Tennessee; the Plateau Research and Education Center (PREC), Crossville and East Tennessee Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant height and biomass yield were measured at maturity, and clonal mass scores were evaluated after harvesting biomass.</li> <li>'File 2' has the genotype name, library, index, total reads, bases, and the Phred quality score (Q30). Young leaf tissue was collected from each F1 progeny and parent, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) procedure. The extracted DNA was genotyped at the USDA-ARS Western Regional Research Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was performed on 951 lines (F1s and their parents) using the PstI-MspI GBS protocol. The quality of these sequences showed that 94.4% of the bases were at or above Q30. Reads were mapped to version 5.0 of the switchgrass reference genome. Single nucleotide polymorphism (SNP) calling was performed, and redundant markers were filtered out for linkage map construction. 'File 3' has SNP ID numbers, SNP locations on chromosomes, map positions, and SNP scores. The cross was used as a four-way cross for QTL analysis, where the male parent Kanlow (K) was assigned as '1', and the female parent Alamo (A) was assigned as '2'.</li> <li>The phased output data from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC, BC, AD, and BD, respectively ('File 3').</li> <li>The progeny file ('File 4') contains the name of the parents used for making crosses and their progenies.</li> <li>A consensus linkage map ('File 5') was produced with Lep-Map3 software. The linkage map contains 18 linkage groups associated with 18 switchgrass chromosomes, marker size (bp), map position (cM) based on male and female maps, and map order.</li> </ul>
Data for: Defining the relationship between phylogeny, clinical manifestation and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations
<p><span>This study looked for correlations between molecular identification, clinical manifestation and morphology for <em>Trichophyton interdigitale</em> and <em>T. mentagrophytes</em>. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Micro- and macromorphology and physiology were analysed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/</span><span>scored phenotypic features, statistically significant differences between species were found only in growth rates at 37°C and in</span><span> the</span><span> production of spiral hyphae but none of these features was diagnostic. </span><span>Correlations were found between <em>T. interdigitale</em> and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis.</span><span> </span><span>The MLST approach showed that ITS genotyping of <em>T. mentagrophytes</em> isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species' names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical </span><span>manifestations and sources</span><span> of infections</span><span>,</span><span> which keep those names alive. This practice is questionable because the use of both names confuses identification</span><span>,</span><span> leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as MALDI-TOF MS fail to distinguish these species. To avoid further confusion and simplify identification in practice, we recommend using the name <em>T. mentagrophytes</em> for the entire complex. When clear differentiation of populations corresponding to <em>T. interdigitale</em> and <em>T. indotineae</em> is possible based on molecular data, we recommend optionally using a variety rank:<em> T. mentagrophytes</em> var. <em>interdigitale</em> and <em>T. mentagrophytes</em> var. <em>indotineae</em>.</span></p>
Data from: Phenotypic clines in herbivore resistance and reproductive traits in wild plants along an agricultural gradient
<p>The conversion of natural landscapes to agriculture is a leading cause of biodiversity loss worldwide. While many studies examine how landscape modification affects species diversity, a trait-based approach can provide new insights into species responses to environmental change. Wild plants persisting in heavily modified landscapes provide a unique opportunity to examine species' responses to land use change. Trait expression within a community plays an important role in structuring species interactions, highlighting the potential implications of landscape mediated trait changes on ecosystem functioning. Here we test the effect of increasing agricultural landscape modification on defensive and reproductive traits in three commonly occurring Brassicaceae species to evaluate plant responses to landscape change. We collected seeds from populations at spatially separated sites with variation in surrounding agricultural land cover and grew them in a greenhouse common garden, measuring defensive traits through an herbivore no-choice bioassay as well as reproductive traits such as flower size and seed set. In two of the three species, plants originating from agriculturally dominant landscapes expressed a consistent reduction in flower size and herbivore leaf consumption. One species also showed reduced fitness associated with increasingly agricultural landscapes. These findings suggest that wild plants are responding to landscape modification, highlighting that species diversity alone does not fully capture the effects of land use change. </p>
Rice phenotypic data – CNA6 population and advanced lines
<p>One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha<sup>-1</sup> per cycle or 67.8 kg.ha<sup>-1</sup> per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1,128 kg.ha<sup>-1</sup>. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.</p>
Data from: Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli
<p><span>Although tag-based donation and recognition have well explained how the cooperative individuals are positively assorted if the cooperative individuals possess some signals and are also able to detect such signals, an additional mechanism is required to explain why some individuals pay the costs of evolving such a tag that may not be rewarded subsequently, and how such tag-based cooperative individuals will meet other similar individuals with a very low mutation rate. Here, we show that many and even all<em> Escherichia coli </em>bacteria cells in the increased antibiotic concentration will plastically evolve to be antibiotic resistant individuals who could protect antibiotic sensitive strain from the attack of antibiotics, and the antibiotic resistant strain could reversibly evolve to be antibiotic sensitive in non-antibiotic supplement medium but in a harsher environment with low glucose. A further experiment showed that antibiotic-sensitive <em>E. coli </em>strain could in turn help reduce the concentration of indole produced by the resistant strain. This metabolic product is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn on the multi-drug exporter to discharge the antibiotic. The utilization of metabolism byproduct indole produced by antibiotic-resistant cells benefits antibiotic-sensitive cells, while the indole-absorbing service of antibiotic sensitive cells unconsciously help in nullifying the indole side effect on antibiotic resistant strain, and a mutual benefit cooperation could therefore evolve.</span></p>
Data from: Phenotypic evolution of SARS-CoV-2: A statistical inference approach
<p>Since its emergence in late 2019, the SARS-CoV-2 virus has spread globally, causing the ongoing COVID-19 pandemic. In the fall of 2020, the Alpha variant (lineage B.1.1.7) was detected in England and spread rapidly, outcompeting the previous lineage. Yet, very little is known about the underlying modifications of the infection process that can explain this selective advantage. Here, we try to quantify how the Alpha variant differed from its predecessor on two phenotypic traits: the transmission rate and the duration of infectiousness. To this end, we analysed the joint epidemiological and evolutionary dynamics as a function of the Stringency Index, a measure of the amount of Non-Pharmaceutical Interventions. Assuming that these control measures reduce contact rates and transmission, we developed a two-step approach based on SEIR models and the analysis of a combination of epidemiological and evolutionary information. First, we quantify the link between the Stringency Index and the reduction in viral transmission. Secondly, based on a novel theoretical derivation of the selection gradient in an SEIR model, we infer the phenotype of the Alpha variant from its frequency changes. We show that its selective advantage is more likely to result from a higher transmission than from a longer infectious period. Our work illustrates how the analysis of the joint epidemiological and evolutionary dynamics of infectious diseases can help understand the phenotypic evolution driving pathogen adaptation.</p>
Genetic and phenotypic data of sexual cross
<p>Genotypic and phenotypic data of offspring from a sexual cross of <em>Aspergillus fumigatus</em> strains AfIR974 and AfIR964. Genotypic data was obtained from Illumina whole genome sequencing off all progeny, and then filtered as described in Auxier et al. 2023. Phenotypic data consists of growth on different nitrogen sources (nitrate (NO3), nitrite (NO2), and hypoxanthine (hx)), which can be used to map the cnx and nia mutations introduced into the two parents using UV mutagenesis. Growth of each offspring was also assessed on 25, 50, and 100 µg/mL of acriflavine as binary states of either growth or no growth.</p> <p>Additionally, the data from Stapley et al. 2017, https://doi.org/10.1098/rstb.2016.0455, is presented in a more useful csv format, which was used in the publication of Auxier et al. 2023.</p> <p>Finally, data from Fernandes et al. 2018, https://doi.org/10.1073/pnas.171307811, was subsetted to include relevant species for comparison in Auxier et al. 2023.</p> <p><span>https://doi.org/10.1073/pnas.171307811</span></p>
Data from: Phenotypic drought stress prediction of European beech (Fagus sylvatica) by genomic prediction and remote sensing
<p><span>Current climate change species response models usually do not include evolution. We integrated remote sensing with population genomics to improve phenotypic response prediction to drought stress in the key forest tree species European beech (<em>Fagus sylvatica</em> L.). We used whole-genome sequencing of pooled DNA from natural stands along an ecological gradient from humid-cold to warm-dry climate. We phenotyped stands for leaf area index (LAI) and moisture stress index (MSI) for the period 2016–2022. We predicted this data with matching meteorological data and a newly developed genomic population prediction score in a Generalised Linear Model. Model selection showed that the addition of genomic prediction decisively increased the explanatory power. We then predicted the response of beech to future climate change under evolutionary adaptation scenarios. A moderate climate change scenario would allow persistence of adapted beech forests, but not worst-case scenarios. Our approach can thus guide mitigation measures, such as allowing natural selection or proactive evolutionary management.</span></p>
Data for Geographic variation in phenotypic divergence between two hybridizing field cricket species
<p><span>Patterns of morphological divergence across species' ranges can provide insight into local adaptation and speciation. In this study, we compare phenotypic divergence among 4,221 crickets from 337 populations of two closely related species of field cricket, <em>Gryllus firmus</em> and <em>G. pennsylvanicus </em>and their hybrids. We find that these species differ across their geographic range in key morphological traits, such as body size and ovipositor length, and we directly compare phenotype with genotype for a subset of crickets to demonstrate nuclear genetic introgression, phenotypic intermediacy of hybrids, and essentially unidirectional mitochondrial introgression. We discuss how these morphological traits relate to life history differences between these two species. Our comparisons across geographic areas support prior research that suggested that cryptic variation within <em>G. firmus</em> may represent different species. Overall, our study highlights how variable morphology can be across wide ranging species, and the importance of studying reproductive barriers in more than one or two transects of a hybrid zone.</span></p>
Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium
<p>Reductions in a limiting nutrient might be expected to necessitate compromises in the functional traits that depend on that nutrient; yet populations existing in locations with low levels of such nutrients often do not show the expected degradation of functional traits. Indeed, we previously found that fish of three species, Logperch (<em>Percina caprodes</em>),Pumpkinseed Sunfish (<em>Lepomis gibbosus</em>), and Yellow Perch (<em>Perca flavescens</em>) residing in low-calcium water in the Upper St. Lawrence River nevertheless maintained levels of scale calcium comparable to those of conspecific populations in high-calcium water. However, it remains possible that the maintenance of one functional trait under nutrient-limited conditions could come at the expense of maintaining other functional traits that depend on that same nutrient. Hence, we here extend prior work by examining other calcium-dependent traits: skeletal element sizes and bone densities in the same fish species in the same area. Using radiographs of 101 fish from the three species across four locations (two in high-calcium water and two in low-calcium water), we document multi-trait "homeostasis" along the gradient of water calcium. That is, we did not detect any effect of calcium regime (low-calcium versus high-calcium) on any of the measured variables. Further, effect sizes for the skeletal traits were very low – lower even than effect sizes previously documented for scale calcium. Our results thus show that native fishes maintain phenotype stability across a suite of functional traits linked to calcium regulation, perhaps pointing to an "organismal-level homeostasis" scenario rather than a "trait-level homeostasis" scenario. </p>
Phenotypic and genetic diversity data recorded in island and mainland populations worldwide
<p><span>We used this dataset to assess the strength of isolation due to geographic and macroclimatic distance across island and mainland systems, comparing published measurements of phenotypic traits and neutral genetic diversity for populations of plants and animals worldwide. </span>The dataset includes 112 studies of 108 species (72 animals and 36 plants) in 868 island populations and 760 mainland populations, with population-level taxonomic and biogeographic information, totalling 7438 records.</p>
Data From: Effects of measurement methods and growing conditions on phenotypic expression of photosynthesis in seven diverse rice genotypes
<p class="p1"><strong>Introduction: </strong>Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (nonsequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the speci<span class="s1">fi</span>c light level.</p> <p class="p1"><strong>Methods: </strong>Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to <span class="s1">fi</span>eld conditions 2-3 days before measurements), and <span class="s1">fi</span>eld environments. We selected seven diverse rice genotypes (<span class="s1">fi</span>ve genotypes from the USDA rice minicore collection: 310588, 310723, 311644, 311677, 311795; and 2 additional genotypes: Nagina 22 and Zhe 733) to understand (1) the limitations of different methods, and (2) phenotypic plasticity of photosynthesis in rice grown under different environments.</p> <p class="p1"><strong>Results:</strong> Our results show that the non-sequential method was time-ef<span class="s1">fi</span>cient and captured more variability of <span class="s1">fi</span>eld conditions than the sequential method, but the model parameters were generally similar between the two methods except for the maximum photosynthesis rate (A<sub>max</sub>). A<span class="s2"><sub>max</sub> </span>was signi<span class="s1">fi</span>cantly lower across all genotypes under greenhouse conditions compared to the growth chamber and <span class="s1">fi</span>eld conditions consistent with prior work, but surprisingly the apparent quantum yield (α) and the mitochondrial respiration (R<sub><span class="s2">d</span></sub>) were generally not different among growing environments or measurement methods.</p> <p class="p1"><strong>Discussion: </strong>Our results suggest that <span class="s1">fi</span>eld conditions are best suited to quantify phenotypic differences across different genotypes, and the nonsequential method was better at capturing the variability in photosynthesis.</p>
Pixelflow Seed Phenotyping Use Case Demo Data
<p>Example 2D and 3D seed phenotyping data for pixelflow use case demo notebooks on the Scivision gallery. Contains original images (.tif) and associated segmented labels of each seed (.npy)</p>
ScienceDex guides
Understand access before you commit
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.