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1,363 results for “phenotypic data”
Data from: Introduced parasite changes host phenotype, mating signal and hybridisation risk: Philornis downsi effects on Darwin's finch song
Introduced parasites that alter their host's mating signal can change the evolutionary trajectory of a species through sexual selection. Darwin's Camarhynchus finches are threatened by the introduced fly Philornis downsi that is thought to have accidentally arrived on the Galapagos Islands during the 1960s. The P. downsi larvae feed on the blood and tissue of developing finches causing on average ~55 % in-nest mortality and enlarged naris size in survivors. Here we test if enlarged naris size is associated with song characteristics and vocal deviation in the small tree finch (Camarhynchus parvulus), the critically endangered medium tree finch (C. pauper), and the recently observed hybrid tree finch group (Camarhynchus hybrids). Male C. parvulus and C. pauper with enlarged naris size produced song with lower maximum frequency and greater vocal deviation, but there was no significant association in hybrids. Less vocal deviation predicted faster pairing success in both parental species. Finally, C. pauper males with normal naris size produced species-specific song, but male C. pauper with enlarged naris size had song that was indistinguishable from other tree finches. When parasites disrupt host mating signal, they may also facilitate hybridisation. Here we show how parasite-induced naris enlargement affects vocal quality resulting in blurred species mating signals.
Data from: Hatching hierarchy but not egg-related effects governs behavioral phenotypes in gull chicks
In many bird species that practice parental care, siblings often compete for resources and care provided by their parents, although their strategies differ according to hatching rank and condition. Differences in offspring strategies are generally attributed to hatching order and maternal effects, which are difficult to separate because these effects are often correlated. For example, third-hatched chicks of large gull species receive more egg testosterones and corticosterone, which influence early behavioral patterns. In this study, we carried out a cross-fostering experiment with first- and last-laid eggs of the yellow-legged gull (Larus michahellis) to test whether the within-brood variation in behavioral strategies for competing with siblings and coping with stress are due to maternal effects or to hatching order. Chicks hatched in the last position within the experimental brood emitted more chatter calls to attract parents' attention, were less prone to respond to warning of danger, and had a lower breathing rate while restrained than first-hatched chicks. Egg laying order did not affect chick behaviors or breathing rate. Thus, we concluded that the different behavioral strategies of chicks were determined by their posthatching experience and not by the original egg position within the clutch. Last-laid eggs were smaller and chicks from those eggs grew slower than chicks from first-laid eggs. Independently of the original laying order, chicks that hatched first in the experimental brood grew faster than their siblings. Overall, our results indicate that behavioral strategies of chicks are plastic and influenced by their early social experience.
Data from: A costly chemical trait: phenotypic condition dependence of cuticular hydrocarbons in a dung beetle
Chemical traits are increasingly recognised as important cues used in mate choice. For example, the cuticular hydrocarbons (CHCs) of insects have been shown to influence mating success in a range of taxa. Less is known, however, about how CHCs are expressed in proportion to an individual's condition, and consequently whether CHCs can function as condition dependent signals of quality. We investigated this question using the dung beetle, Onthophagus taurus. CHCs are subject to sexual selection in this species through mate choice. A dietary manipulation revealed condition dependence of CHC expression for both sexes: dietary restriction decreased overall CHC production and altered the composition of CHCs. Furthermore, CHC production was associated with a measure of condition in beetles fed a limited diet but not those fed ad libitum. These results implicate a resource cost to CHC production that is likely to result in trade-offs with other fitness components in this species, as these respond similarly to a dietary restriction. The CHC profiles showed sexual dimorphism: males produced more CHCs and the sexes differed in the blend of compounds they produced. There was evidence for a male dimorphism in the CHC profile, in line with the presence of the alternative reproductive tactics (minor sneaks and major fighters) in this species. However, rather than mimicking a female CHC profile, minor males differed more from females than major males. Our results suggest that CHCs are a costly trait in O. taurus that has the potential to act as a condition dependent signal of quality.
Data from: Thrifty phenotype vs cold adaptation: trade-offs in upper limb proportions of Himalayan populations of Nepal
The multi-stress environment of high altitude has been associated with growth deficits in humans, particularly in zeugopod elements (forearm, lower leg). This is consistent with the thrifty phenotype hypothesis, which has been observed in Andeans, but has yet to be tested in other high altitude populations. In Himalayan populations, other factors, such as cold stress, may shape limb proportions. The current study investigated whether relative upper limb proportions of Himalayan adults (n=254) differ between highland and lowland populations, and whether cold adaptation or a thrifty phenotype mechanism may be acting here. Height, weight, humerus length, ulna length, hand length, and hand width were measured using standard methods. Relative to height, total upper limb and ulna lengths were significantly shorter in highlanders compared to lowlanders in both sexes, whilst hand and humerus length were not. Hand width did not significantly differ between populations. These results support the thrifty phenotype hypothesis, as hand and humerus proportions are conserved at the expense of the ulna. The reduction in relative ulna length could be attributed to cold adaptation, but the lack of difference between populations in both hand length and width indicate that cold adaptation is not shaping hands proportions in this case.
Denoising Autoencoders for Phenotype Stratification (DAPS) Sample Trained Simulated Patient Data
<p>DAPS Trained data</p>
Denoising Autoencoders for Phenotype Stratification (DAPS) Sample Trained Patient Data
<p>Data for: https://github.com/greenelab/DAPS</p>
Tara Pacific Biomarker-Based Coral Phenotype Data Release - Pocillopora
<p>Those data correspond to the measurements of the phenotype signatures of <em>Pocillopora </em>colonies collected through 30 Pacific Islands. More precisely, six different biomarkers have been measured for each colony: Animal biomass, Symbiont biomass (normalized by milligram of protein and by centimeter squared), protein carbonylation, total antioxydant capacity, total carbohydrate content and mitochondrial DNA copy number.</p> <p>(XLS version with methodological references)</p>
Phenotypic and genotypic data of genomic selection study of spring frost tolerance of Norway spruce
Open the record for dataset details and reuse information.
Figure 2 in Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops)
Figure 2. Bothrops oligobalius sp. nov. from French Guiana. Photo by Maël Dewynter.
Phenotypic and marker data for statistical genetic analysis of Minnesota maize lines
<p>Publicly available maize lines are a resource for studying quantitative genetic variation in plants. This dataset includes cluster or subpopulation information, phenotypic data, and single nucleotide polymorphism (SNP) data for 272 maize lines developed by the University of Minnesota, other universities, and seed companies. The lines were evaluated at multiple locations in Minnesota in 2011 and 2012 for different phenological, morphological, and kernel composition traits. The lines were genotyped for 56,110 SNP loci on the Maize SNP50 Beadchip (Illumina). Filtering for SNP data quality led to data for 28,626 SNP loci for the 272 maize lines. Population structure analysis showed that the maize lines clustered into five subpopulations (A321 or Minnesota 13, B73, Mo17, Oh43, and PH207 or Iodent) that represented most of the U.S. Corn Belt diversity (Schaefer and Bernardo 2013a, Crop Science 53:1529-1536). Genomewide association mapping revealed marker-trait associations for male flowering date, female flowering date, plant height, ear height, and kernel concentration for oil, protein, and starch (Schaefer and Bernardo 2013b, Crop Science 53:2518-2529). The covariance between relatives is a tenet in quantitative genetics, but such classical theory has ignored any resemblance between individuals unrelated by pedigree. Analysis of this maize dataset showed that a covariance between nonrelatives in maize is not ubiquitous but it is sometimes rpesent for specific traits and for certain groups of unrelated individuals (Bernardo 2022, Heredity).</p>
Phenotypic data for the Sorghum bicolor core collection selected from the whole collection in the Uganda National GeneBank
<p>Passport data for the Sorghum bicolor core collection selected from the whole collection in the Uganda National GeneBank (Information is based on 286 core collection accessions, excluding 24 accessions which did not germinate in this trial</p>
Data from: Phenotypic determinants of inter-individual variability of litter consumption rate in a detritivore population
Abstract not entered
Data from: A time series model for estimating temporal variation in phenotypic selection on laying dates in a Dutch great tit population
[No abstract entered]
Supporting Data:A pleiotropic 'stretch' phenotype is associated with metaxylem vessel element length, axial hydraulic conductance, root elongation, water utilization, and drought adaptation in maize.
<p>These data were collected to assess how xylem perforation plates affect water use strategies in maize (<em>Zea mays </em>L.) under water deficit through empirical studies in controlled environments and in the field. In this work, our goals were to explore the extent of intraspecific variation for the structure of perforation plates within an annual monocot and assess how this variation affects transport and use of water under drought stress. Specifically, we test the hypotheses that (1) simple perforation plates have a significant effect on water transport, (2) intraspecific variation exists for these features in maize, and (3) this variation affects water use strategies under drought stress. </p>
Phenotype data Eucalyptus wood properties CNB Cirad-Ufla
<p>Phenotypic data obtained by NIR prediction on wood of the studied trees (5 trees for 10 clones of CENIBRA in 3 sites in Brazil) : wood density, stiffness and microfibril angle of cell walls</p> <p> </p>
Data from: Experimentally evolved and phenotypically plastic responses to enforced monogamy in a hermaphroditic flatworm
Sexual selection is considered a potent evolutionary force in all sexually reproducing organisms, but direct tests in terms of experimental evolution of sexual traits are still lacking for simultaneously hermaphroditic animals. Here, we tested how evolution under enforced monogamy affected a suite of reproductive traits (including testis area, sex allocation, genital morphology, sperm morphology and mating behaviour) in the outcrossing hermaphroditic flatworm Macrostomum lignano, using an assay that also allowed the assessment of phenotypically plastic responses to group size. The experiment comprised 32 independent selection lines that evolved under either monogamy or polygamy for 20 generations. While we did not observe an evolutionary shift in sex allocation, we detected effects of the selection regime for two male morphological traits. Specifically, worms evolving under enforced monogamy had a distinct shape of the male copulatory organ and produced sperm with shorter appendages. Many traits that did not evolve under enforced monogamy showed phenotypic plasticity in response to group size. Notably, individuals that grew up in larger groups had a more male-biased sex allocation and produced slightly longer sperm than individuals raised in pairs. We conclude that, in this flatworm, enforced monogamy induced moderate evolutionary but substantial phenotypically plastic responses.
Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response
Background: Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has not been studied. Results: Here, we describe the mapping of quantitative trait loci (QTL) for constitutive and damage induced trichome density in two new recombinant inbred line populations of A. thaliana; mapping for constitutive and induced trichome density also allowed for the investigation of damage response (plasticity) QTL. Both novel and previously identified QTL for constitutive trichome density and the first QTL for induced trichome density and response are identified. Interestingly, two of the four parental accessions and multiple RILs in each population exhibited lower trichome density following leaf damage, a response not previously described in A. thaliana. Importantly, a single QTL was mapped for the response phenotype and allelic variation at this locus appears to determine response trajectory in RILs. The data also show that epistatic interactions are a significant component of the genetic architecture of trichome density. Conclusions: Together, our results provide further insights into the genetic architecture of constitutive trichome density and new insights into induced trichome density in A. thaliana specifically and to our understanding of the genetic underpinnings of natural variation generally.
Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Data from: The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes
The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, e.g. in the Central American Midas Cichlid assemblage. Here we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach-content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of mollusks and invertebrates. We then used comparative Illumina RNA sequencing of thick versus normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.
Data from: Ecotypic divergence in Crepis tectorum (Asteraceae): inferring trait lability and correlational constraints from hormonally manipulated phenotypes
Despite long-standing interest in the evolutionary role of plant hormones, relatively few studies have used hormonally manipulated phenotypes to address questions about phenotypic evolution in plants. In the present investigation, I subjected plants of Crepis tectorum subsp. pumila to simple gibberellin (GA) treatments under both field and greenhouse conditions to assess developmental lability and correlational constraints of phenotypic traits that distinguish this dwarf ecotype from conspecific populations of the much taller weed ecotype (subsp. tectorum). The hormonally manipulated plants largely phenocopied the weed ecotype in leaf shape, plant stature and branching habit, indicative of both high lability and tight integration of traits reflecting gross morphology. Floral size traits sometimes declined after GA application, especially under field conditions. The latter result conflicts with the positive correlations between floral and vegetative size traits seen in previous comparative analyses and point to a tradeoff that could act as a constraint on ecotype divergence. The response to GA was consistent in direction for most traits, as opposed to the magnitude of response, which varied depending on the trait, the population, the growing environment, and the timing and level of hormone application. Taken together, the results highlight the potential for simple hormonal changes to cause large, plastic shifts in phenotype, but also illustrate the constrained nature of such influences.
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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.