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164 results for “phenotypic diversity”
Data from: Genetic admixture increases phenotypic diversity in the nectar yeast Metschnikowia reukaufii,
<p>Raw data and supplementary files for the manuscript "Genetic admixture increases phenotypic diversity in the nectar yeast <em>Metschnikowia reukaufii</em>."</p> <p>-------------------</p> <p><strong>Table S5.xlsx </strong>-- Pairwise correlations between phenotypic traits of <em>Metschnikowia reukaufii</em>.</p> <p><strong>Table S6.xlsx</strong> -- Detailed results obtained in tests of phylogenetic signal for different phenotypic traits and indices of overall performance of <em>Metschnikowia reukaufii</em>.</p> <p><strong>Table S7.xlsx</strong> -- Detailed model fitting results obtained for phenotypic traits and indices of overall performance of <em>Metschnikowia reukaufii</em>.</p> <p><strong>mronlyvcf-renamed.vcf</strong> -- High coverage SNPs obtained from whole genome mapping of 73 <em>Metschnikowia reukaufii</em> strains to diploid reference (mean coverage = 47.9×, range 23 – 116×).</p> <p><strong>MR_phenotypes.xlsx</strong> -- Phenotypic data obtained for 73 <em>Metschnikowia reukaufii</em> strains.</p>
Phenotypic diversity of root architecture and genotypic variation in durum wheat under salt stress
<p>Supplementary data consists of Principal Components values for traits detected under salt and control conditions (S1); Markers' locations onto the durum wheat reference genome associated with QTL (S2); Markers associated with genes from NCBI database (S4); PCR results and alleles distribrution</p>
Fig. 2 and table 3 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 2 and table 3 illustrate the values of PCA loadings for the morphometrics of Clarias gariepinus obtained from the four Rivers showing Pre-ventral distance (PVD) as the trait with the highest variation.
Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex
<p class="MsoNormal"><span>Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid <em>Arabidopsis suecica </em>and its parent species <em>A. arenosa</em> and <em>A. thaliana</em> were chosen as a model system to investigate relationships between phenotypic plasticity, fitness and genetic variation. Particularly, we test if <em>A. suecica</em> is more plastic, show higher genetic diversity and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water and light, while genetic diversity was assessed through analysis of AFLP markers. <em>Arabidopsis arenosa</em> showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity were found in the inbreeding <em>A. thaliana</em>. Geographic spacing of populations might explain the clear genetic structure in <em>A. arenosa</em>, while the lack of structure in <em>A. suecica </em>could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed towards <em>A. arenosa</em> having lower fitness under poor environmental conditions. <em>Arabidopsis </em><em>suecica</em>, on the other hand, showed tendencies towards keeping up fitness under different environmental conditions. </span></p>
UV mutagenesis conjugated to high throughput screening as a tool to generate new phenotypic diversity in wine yeast
<p><strong>The current global changes, societal and climatic, strongly challenge the wine industry. Multiple methods are applied in the development of new strains for the industry, but many are based on the existing phenotypic and genetic diversities. UV mutagenesis, as an untargeted strategy, has been successfully used for years, with significant examples on wine. Here we developed and validated a UV-mutant generation strategy coupled with a high throughput screening in wine-like conditions. This strategy led to the production of a 502 mutant’s library for which concentrations of eight primary metabolites after fermentation were assessed. This data paper presents the resulting data.</strong></p>
Figure 6 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 6. Scatterplot of individual scores from the canonical variate analysis (CVA) of female specimens of: A, sympatric populations of Merodon avidus A and M. avidus B from Dubašnica Mt (ADUB, BDUB) and Greece (AGRE, BGRE) (Wilks' L = 0.003; F(48,30) = 3.64; P <0.001); B, allopatric populations of M. avidus A from FYR MACEDONIA (AMKD), Morinj (AMOR), and the Pannonian region (APAN) (Wilks' L = 0.09; F(32,48) = 3.59; P <0.0001); C, allopatric populations of M. avidus B from Durmitor Mt (BDUR), Stara Mt (BSPL), Kopaonik Mt (BKOP), and FYR MACEDONIA (BMKD) (Wilks' L = 0.36; F(32,32) = 0.66; P <0.879); D, allopatric populations of M. avidus A and M. avidus B (Wilks' L = 0.09; F(80,245) = 1.94; P <0.0001). The amount of variation explained by each canonical axis is in parentheses.
Figure 5 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 5. Scatterplot of individual scores from the canonical variate analysis (CVA) of all specimens (both sexes) of metapopulations: A, Merodon avidus A from Dubašnica Mt (ADUB) (Wilks' L = 0.04; F(48,72) = 3.06; P <0.000); B, M. avidus B from Dubašnica Mt (BDUB) (Wilks' L = 0.10; F(64,174) = 2.18; P <0.000); C, M. avidus B from Durmitor Mt (BDUR) (Wilks' L = 0.10; F(64,174) = 2.21; P <0.000); D, M. avidus A from FYR MACEDONIA (AMKD) (Wilks' L = 0.002; F(112,171) = 2.40; P <0.000); E, M. avidus A from Greece (AGRE) (Wilks' L = 0.009; F(64,53) = 1.93; P <0.007). The amount of variation explained by each canonical axis is in parentheses. The number of misclassified specimens/total number of analysed
Figure 1 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 1. Origin of the analysed populations using wing geometric morphometrics from the Balkan Peninsula: 1, Pannonian Plain (PAN, Serbia); 2, Dubašnica Mt, E 21°59′, N 44°01′ (DUB, Serbia); 3, Stara Mt, E 22°41′, N 43°20′ (SPL, Serbia); 4, Kopaonik Mt, E 20°40′, N 43°15′ (KOP, Serbia); 5, Durmitor Mt, E 19°00′, N 43°11′ (DUR, Montenegro); 6, Morinj, E 18°40′, N 43°29′30″ (MOR, Montenegro); 7, Former Yugoslav Republic of Macedonia (MKD); 8, Greece (GRE). (Numbers within region are noted sampling sites of populations).
Data from: Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming
<p>Premise of the study: The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare <em>Boechera perstellata</em> (Braun's rockcress) and widespread <em>B. laevigata</em> to acclimate to change.</p> <p>Methods: We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of <em>B. perstellata</em> and <em>B. laevigata</em> propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential.</p> <p>Key results: Plasticity was limited in both rare <em>B. perstellata</em> and widespread <em>B. laevigata</em>, but differences in the plasticity of root traits between species suggest that <em>B. perstellata</em> may have less capacity to acclimate to change. In contrast to its widespread congener, <em>B. perstellata</em> exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, <em>B. perstellata</em> also had lower levels of observed heterozygosity than <em>B. laevigata</em> at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among <em>B. laevigata</em> populations.</p> <p>Conclusions: Overall, the ability of phenotypic plasticity to broadly explain the rarity of <em>B. perstellata</em> vs. commonness of <em>B. laevigata </em>is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of <em>B. perstellata</em> and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.</p>
Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex
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Data from: Coincident transitions across elevation and origins of functional innovations drove the phenotypic and ecological diversity of lungless salamanders
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Data from: Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming
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Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards
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Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)
<p>Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (<i>Etheostoma caeruleum</i>) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.</p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
Learning‐induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress
<p>Aphid populations frequently include phenotypes that are resistant to parasitism by hymenopterous parasitoid wasps, which is often attributed to the presence of 'protective' facultative endosymbionts residing in aphid tissues, particularly <em>Hamiltonella defensa</em>. In field conditions, under parasitoid pressure, the observed coexistence of aphids with and without protective symbionts cannot be explained by their difference in fitness alone.</p> <p>Using the cereal aphid <em>Rhopalosiphum padi</em> as a model, we propose an alternative mechanism whereby parasitoids are more efficient at finding common phenotypes of aphid and experience a fitness cost when switching to the less common phenotype.</p> <p>We construct a model based on delay differential equations and parameterise and validate the model with values within the ranges obtained from experimental studies. We then use it to explore possible effects on system dynamics under conditions of environmental stress, using our existing data on the effects of drought stress in crops as an example.</p> <p>We show the 'switching penalty' incurred by parasitoids leads to stable coexistence of aphids with and without <em>H. defensa</em> and provides a potential mechanism for maintaining phenotypic diversity amongst host organisms. We show that drought-induced reduction in aphid development time has little impact. However, greater reduction in fecundity on droughted plants of symbiont-protected aphids can cause insect population cycles when the system would be stable in the absence of drought stress.</p> <p>The stabilising effect of the increased efficiency in dealing with more commonly encountered host phenotypes is applicable to a broad range of consumer-resource systems and could explain stable coexistence in competitive environments. The loss of stable coexistence when drought has different effects on the competing aphid phenotypes highlights the importance of scenario testing when considering biocontrol for pest management.</p>
Data from: Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes
<p>Phenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide first-hand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data, and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often overlooked material such as field notes, for evolutionary and ecological research.</p>
Hair phenotype diversity across Indriidae lemurs
<p><strong><span>Objectives: </span></strong><span>Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (<em>Avahi</em>, <em>Indri</em>, <em>Propithecus</em>)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun).</span></p> <p><strong><span>Materials and Methods: </span></strong><span>Our analyses considers multiple phylogenetic scales (family-level, genus-level) and hypotheses (e.g., Gloger's rule, the body cooling hypotheses). We obtain hair color and density from museum and/or wild animals, opsin genotypes from wild animals, and climate data from WorldClim. To analyze our data, we use </span>phylogenetic generalized linear mixed models (PGLMM) using Markov chain Monte Carlo algorithms.</p> <p><strong><span>Results: </span></strong><span>Our results show that across the Indriidae family, darker hair is typical in wetter regions. However, within <em>Propithecus</em>, dark black hair is common in colder forest regions. Results also show pelage redness increases in populations exhibiting enhanced color vision. Lastly, we find follicle density on the crown and limbs increases in dry and open environments. </span></p> <p><strong><span>Discussion: </span></strong><span>This study highlights how different selective pressures across distinct phylogenetic scales have likely acted on primate hair evolution. Specifically, our data across <em>Propithecus</em> may implicate thermoregulation and is the first empirical evidence of Bogert's rule in mammals. Our study also provides rare empirical evidence supporting an early hypothesis on hominin hair evolution. </span></p>
Fig. 4 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 4. PCA loadings for meristics of Clarias gariepinus obtained from the four rivers.
Fig. 2 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 2. PCA loadings for the morphometrics of Clarias gariepinus obtained from the four rivers.
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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
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