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6,234 results for “phenotypes”
Phenotypic divergence in two sibling species of shorebird: Common Snipe and Wilson's Snipe (Charadriiformes: Scolopacidae)
<p><span><span><span><span><span><span><span><span><span><span><span>Natural selection and social selection are among the main shapers of biological diversity, but their relative importance in divergence remains understudied. Additionally, although neutral evolutionary processes may promote phenotypic divergence, their potential contribution in speciation is often overlooked in studies of comparative morphology. In this study, we investigated phenotypic differentiation in two allopatric shorebirds: the Palearctic Common Snipe <i>Gallinago gallinago</i> and the Nearctic Wilson's Snipe <i>G. delicata</i>. Specimens of Common Snipe (n = 355 skins, n = 163 skeletons) and Wilson's Snipe (n = 403 skins, n = 141 skeletons) in natural history collections, were examined to quantify differences in skeletal and external measurements, and measures on wing and tail plumage variables. The species did not differ in skeletal variables except for the relatively larger sternum of the Common Snipe. The two species do not differ in multivariate wing size or shape (pointedness). Previously known plumage differences between these species were confirmed: the Common Snipe has fewer rectrices, longer and wider outermost rectrices, more extensive white on tips of the secondary feathers, and more white in the axillaries. Between-species variance in skeleton, primary length, and plumage variables was greater than expected if drift was mainly responsible for phenotypic divergence, suggesting a role of selective processes. However, drift could not be rejected after adjusting for multiple comparisons. Differences in plumage traits were greater than in skeletal or external measurements. Because snipe use plumage traits in signalling, the results suggest a faster divergence between these species in socially selected traits than in those related to resource use.</span></span></span></span></span></span></span></span></span></span></span></p>
Trait-fitness associations do not predict within-species phenotypic evolution over 2 million years
Long-term patterns of phenotypic change are the cumulative results of tens of thousands to millions of years of evolution. Yet, empirical and theoretical studies of phenotypic selection are largely based on contemporary populations. The challenges in studying phenotypic evolution, in particular trait-fitness associations in the deep past, are barriers to linking micro- and macroevolution. Here, we capitalize on the unique opportunity offered by a marine colonial organism commonly preserved in the fossil record to investigate trait-fitness associations over 2 million years. We use the density of female polymorphs in colonies of <em>Antartothoa tongima</em> as a proxy for fecundity, a fitness component, and investigate multivariate signals of trait-fitness associations in six time intervals on the backdrop of Pleistocene climatic shifts. We detect negative trait-fitness associations for feeding polymorph (autozooid) sizes, positive associations for autozooid shape but no particular relationship between fitness and brood chamber size. In addition, we demonstrate that long-term trait patterns are explained by palaeoclimate and to a lesser extent by ecological interactions. Our analyses show that macroevolutionary outcomes of trait evolution are not a simple scaling-up from the trait-fitness associations.
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
<p>Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a pre-specified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.</p>
Data from: The Odonate Phenotypic Database, a new open data resource for comparative studies of an old insect order
<p>We present The Odonate Phenotypic Database (OPD): an online data resource of dragonfly and damselfly phenotypes (Insecta: Odonata). Odonata is a relatively small insect order that currently consists of about 6400 species belonging to 32 families. The database consists of a variety of morphological, life-history and behavioral traits, and biogeographical information collected from literature sources. We see taxon-specific phenotypic databases from Odonata and other organismal groups as becoming an increasing valuable resource in comparative studies. Our database has phenotypic records for 1011 of all 6400 known odonate species. The database is accessible at <a href="http://www.odonatephenotypicdatabase.org/">http://www.odonatephenotypicdatabase.org/</a> and also uploaded as a supporting information file with this paper.</p> <p><strong>Update on November 6 2020</strong></p> <p>A total of 397 new taxa have been added to the database (aside from wing pigmentation data, many taxa have information on morphology, distribution and behaviour).</p> <p>Updated (validated) pigmentation status for 20 taxa (for these taxa, columns concerning wing pigment have been changed compared to the original opdb‐file, while all other columns have not been changed).</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>
Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?
<p>Pathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. <span>To address</span> biological complexity below the species level<span>, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr <i>Salvelinus namaycush</i> ecotypes in Rush Lake, USA. </span>A rapid phenotypic shift in body and head shape was found within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (ages 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing changes in growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.</p>
Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule
<p>Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch's rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In this paper we derive a multivariate equivalency for investigating trends in sexual dimorphism – relative to overall body size – across taxa and provide a generalized test to determine whether such allometric patterns correspond with Rensch's rule. For univariate linear traits like body size, our approach yields equivalent results to those from standard procedures, but our test is also capable of detecting trends in multivariate datasets like shape. Computer simulations reveal the method displays appropriate statistical properties, and an empirical example in Mediterranean lizards provides the first demonstration of Rensch's rule in a multivariate phenotype (head shape). Our generalized procedure substantially extends the analytical toolkit for investigating macroevolutionary patterns of sexual dimorphism and seeking a better understanding of the processes that underlie them.</p>
Applying RGB- and Thermal-Based Vegetation Indices from UAVs for High-Throughput Field Phenotyping of Drought Tolerance in Forage Grasses
<p>Basic data from publication <a href="https://doi.org/10.3390/rs13010147">https://doi.org/10.3390/rs13010147</a></p> <p><strong>All_TDRdata.csv</strong> contains the data from 48 TDR sensors (30 cm) installed in the three rainout shelters.</p> <ul> <li>Sensors 1 - 18 were installed vertically to obtain soil moisture content averaged over the 10 - 40 cm profile, on 6 locations per shelter</li> <li>Sensors 19-21 were installed diagonally to obtain soil moisture content averaged over the 20 - 40 cm profile on one location per shelter</li> <li>Sensors 22-24 were installed diagonally to obtain soil moisture content averaged over the 40 - 60 cm profile on one location per shelter</li> <li>Sensors 25-27 were installed horizontally to obtain soil moisture content at 10 cm depth on one location per shelter</li> <li>Sensors 28-30 were installed horizontally to obtain soil moisture content at 20 cm depth on one location per shelter</li> <li>Sensors 31-33 were installed horizontally to obtain soil moisture content at 30 cm depth on one location per shelter</li> <li>Sensors 34-36 were installed horizontally to obtain soil moisture content at 40 cm depth on one location per shelter</li> <li>Sensors 37-39 were installed horizontally to obtain soil moisture content at 50 cm depth on one location per shelter</li> <li>Sensors 40-42 were installed horizontally to obtain soil moisture content at 60 cm depth on one location per shelter</li> <li>Sensors 43-45 were installed horizontally to obtain soil moisture content at 70 cm depth on one location per shelter</li> <li>Sensors 46-48 were installed horizontally to obtain soil moisture content at 80 cm depth on one location per shelter</li> </ul> <p>Climate.txt contains the daily averaged microclimatic data</p> <p>PhenotypingData.csv contains the phenotypic data from the UAV flights and the breeder scores</p> <p> </p>
Granja et al. GSE139369 mixed-phenotype acute leukemia for Besca
<p>The gene expression matrices were downloaded from GEO (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139369">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139369</a>), originally published by Granja JM, Klemm S, McGinnis LM, Kathiria AS et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol 2019 Dec;37(12):1458-1465. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31792411">31792411</a>.</p> <p>Individual raw matrices were merged to be uploaded directly with Besca.</p> <p>We then reprocessed the dataset using the Besca package (https://github.com/bedapub/besca).</p> <p> </p> <p>Raw processed h5ad is available.</p> <p>Processed and annotated h5ad was annotated using the notebook available at </p> <p><a href="https://github.com/bedapub/besca_publication_results/tree/master/hematopoietic/Granja2019">https://github.com/bedapub/besca_publication_results/tree/master/hematopoietic/Granja2019</a></p> <p>Citeseq data raw data is available under <a href="https://zenodo.org/api/files/abfb5567-6a8b-4c57-8d76-c22753433b10/Granja2019_adt_raw.h5ad?versionId=2f3276b6-41b1-48ad-aad2-f9bd04f61bfd">Granja2019_adt_raw.h5ad</a>. The results of CLR/DSB normalization with it associated clustering and UMAP were added to the annotated h5ad file.</p> <p> </p> <p> </p>
Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation
<p>Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue-, and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here we examine whether traits that are integrated at the phenotypic level, also exhibit a shared genetic basis (e.g., pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium, and ventricle respectively) from an F<sub>5</sub> hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric- from asymmetric-components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.</p>
Staphylococcus aureus isolated from ruminants with mastitis in northern Greece dairy herds: genetic relatedness and phenotypic and genotypic characterization
<p>Figure S1: Dendrogram of SmaI PFGE pulsotypes (P) and characteristics of the 162 S. aureus isolates.</p>
Allostery through DNA drives phenotype switching
<p>Allostery is a pervasive principle to regulate protein function. Here, we show that DNA also transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in <em>Bacillus subtilis</em> requires an all-or-none promoter binding of multiple ComK proteins. Using single-molecule FRET, we find that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which paves new ways to design the dynamic properties of genetic circuits.</p>
Genetic and phenotypic variation in Bathygobius cocosensis from East Australia (2014–2016)
<p>Genetic and phenotypic data from an East Australian metapopulation of the intertidal goby, <em>Bathygobius cocosensis </em>(Bleeker 1854). Data was collected over three years (2014–2016) from juveniles and adult subpopulations at three sites: Point Cartwright, Hastings Point and Shellharbour. Genetic variation was characterised using genome-wide SNPs, obtained through pooled ezRAD sequencing. Phenotypic variation was characterised using geometric morphometric analysis of head shape morphology. The analyses contained in this repository are for a manuscript submitted to <em>Molecular Ecology</em>.</p>
Data from: Nutritional imbalance suppresses migratory phenotypes of the Mongolian locust (Oedaleus asiaticus)
For many species, migration evolves to allow organisms to access better resources. However, the proximate factors that trigger these developmental changes, and how and why these vary across species, remain poorly understood. One prominent hypothesis is that poor-quality food promotes development of migratory phenotypes and this has been clearly shown for some polyphenic insects. In other animals, particularly long-distance bird migrants, it is clear that high-quality food is required to prepare animals for a successful migration. We tested the effect of diet quality on the flight behaviour and morphology of the Mongolian locust, Oedaleus asiaticus. Locusts reared at high population density and fed low-N grass (performance-enhancing for this species) had enhanced migratory morphology relative to locusts fed high-N grass. Furthermore, locusts fed synthetic diets with an optimal 1 : 2 protein : carbohydrate ratio flew for longer times than locusts fed diets with lower or higher protein : carbohydrate ratios. In contrast to the hypothesis that performance-degrading food should enhance migration, our results support the more nuanced hypothesis that high-quality diets promote development of migratory characteristics when migration is physiologically challenging.
Data from: Phenotype-environment matching predicts both positive and negative effects of intraspecific variation
Natural populations can vary considerably in their genotypic and/or phenotypic diversity. Differences in this intraspecific diversity can have important consequences for contemporary ecological dynamics, but the direction and magnitude of these effects appear inconsistent across studies and systems. Here we proposed and tested the hypothesis that context-dependent ecological effects of altering phenotypic variance are predictable and arise from the relationship between a population's mean phenotype and the local environmental optimum. By factorially manipulating the mean and variance of a key host trait in environments with and without a lethal parasite, we demonstrate that increasing phenotypic variance can have beneficial effects for host populations (e.g. smaller disease epidemics), but only when the population's initial phenotype was poorly-matched to the local environment. When phenotypes were initially well-suited to environmental conditions, in contrast, greater phenotypic variance led to larger disease epidemics. Significant reductions in individual susceptibility occurred in both contexts over time, but the mechanisms leading to those reductions differed; strong selection was caused by either a 'suboptimal' trait mean and insufficient trait variance, or a 'near-optimal' trait mean and too much trait variance. Increasing intraspecific variation is clearly not always beneficial for populations, instead producing predictable ecological and evolutionary effects that depend on environmental context and biological interactions.
Data from: A resource on latitudinal and altitudinal clines of ecologically relevant phenotypes of the Indian Drosophila
The unique geography of the Indian subcontinent has provided diverse natural environments for a variety of organisms. In this region, many ecological indices such as temperature and humidity vary predictably as a function of both latitude and altitude; these environmental parameters significantly affect fundamental dynamics of natural populations. Indian drosophilids are diverse in their geographic distribution and climate tolerance, possibly as a result of climatic adaptation. These associations with environmental parameters are further reflected in a large number of clines that have been reported for various fitness traits along these geographical ranges. This unique amalgamation of environmental variability and genetic diversity make the subcontinent an ecological laboratory for studying evolution in action. We assembled data collected over the last 20 years on the geographical clines for various phenotypic traits in several species of drosophilids and present a web-resource on Indian-Drosophila ( http://www.indian-drosophila.org/). The clinal data on ecologically relevant phenotypes of Indian drosophilids will be useful in addressing questions related to future challenges in biodiversity and ecosystems in this region.
Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa
The interbreeding of two species after a period of separation (secondary contact) most often results in stable areas of hybridization or tension zones characterized by selection against hybrid individuals. Three plumage forms of Zosterops meet and interbreed in central South Africa. Here we examine how phenotypic measures (biometric and plumage) and genotypic markers (mitochondrial and nuclear DNA) change through a putative hybrid zone located in the area where the ranges of the Orange River white-eye Zosterops pallidus and a subspecies of the Cape white-eye Zosterops virens capensis meet. Four of the five sequenced loci (i.e. ATP6, MUSK, GADPH and TGF-β2) showed strong divergence and differentiation between allopatric parental populations, whereas the sex-linked CHD1Z locus exhibited high homogeneity. Microsatellite data also distinguished between pure Z. pallidus and Z. v. capensis populations. Together, the nuclear data (introns and microsatellites) identified at least 12 hybrid individuals as later generation hybrids (i.e. F2 or backcrosses), and no F1 hybrids were detected. As genetic incompatibility does not appear to play a role in restricting this stable hybrid zone, it is likely that environmental conditions including biome type and edge effect are constraining hybrid zone movement.
Data from: Mate availability determines use of alternative reproductive phenotypes in hermaphrodites
<p>In many species individuals can employ alternative reproductive phenotypes, with profound consequences for individual fitness and population dynamics. This is particularly relevant for self-compatible hermaphrodites, which have exceptionally many reproductive options. Here we investigated the occurrence of reproductive phenotypes in the simultaneously hermaphroditic freshwater snail <i>Radix balthica</i> under experimentally simulated conditions of low vs. moderate population density. We captured all mating behavior on camera and measured individual female lifetime reproductive success. We found every possible reproductive phenotype: (1) both male and female (i.e. truly hermaphroditic) reproduction, (2) purely female and (3) purely male reproduction, (4) male reproduction combined with self-fertilization and (5) female mating activity, (6) pure self‑fertilization without mating and (7-8) two types of reproductive failure. Variation in alternative reproductive phenotypes was explained by mate availability (10.8%) and individual condition, approximated by a snail's mean daily growth rate (17.5%). Increased mate availability resulted in a lower diversity of reproductive phenotypes, in particular increasing the frequency of true hermaphrodites. However, it lowered phenotype-specific fecundities and hence reduced the population growth rate. Snails in better condition were more likely to reproduce as true hermaphrodites or pure females, while low-condition snails tended to suffer reproductive failure. Overall, we show substantial variation in alternative reproductive phenotypes in a hermaphrodite, which is possibly in part maintained by fluctuations in population density and thus mate availability, and by variation in individual condition. We also provide evidence of an almost two-fold increase in clutch size that can be ascribed specifically to mating as a female.</p>
Data for 'Phenotypic plasticity and genetic variation in leaf traits of Yushania niitakayamensis (Bambusoideae; Poaceae) in contrasting light environments'
<p>This is the Data for the article entitled 'Phenotypic plasticity and genetic variation in leaf traits of Yushania niitakayamensis (Bambusoideae; Poaceae) in contrasting light environments' submitted to 'Journal of Plant Research'</p> <p><a href="https://doi.org/10.1007/s10265-021-01327-y">https://doi.org/10.1007/s10265-021-01327-y</a></p> <p>Traits' names are listed below:</p> <p>Leaf length (LL), Leaf width (LW), Specific leaf area (SLA), Stomatal density (SD), Leaf thickness (LT), Relative frequency of cavities formed by the collapsed fusoid cells (CFC), Leaf chlorophyll content per unit area ([Chl]area), Ratio of chlorophyll a to chlorophyll b (Chl a/b), Leaf nitrogen content per unit area ([N]area), Leaf stable carbon isotope ratio (δ13C), Photosynthetic photon flux density (PPFD), Actual quantum yield of PSII electron transport (ΦPSII), Electron transport rate (ETR), Light-saturated photosynthetic rate (Asat), Stomatal conductance (gs), Dark respiration rate (Rd), Apparent quantum yield (AQY), The ratio of intercellular to ambient CO2 concentration (Ci/Ca), Photosynthetic water use efficiency (WUE)</p>
Data from: Phenotypic selection on floral traits in an urban landscape
Native species are increasingly living in urban landscapes associated with abiotic and biotic changes that may influence patterns of phenotypic selection. However, measures of selection in urban and non-urban environments, and exploration of the mechanisms associated with such changes, are uncommon. Plant-animal interactions have played a central role in the evolution of flowering plants and are sensitive to changes in the urban landscape, and thus provide opportunities to explore how urban environments modify selection. We evaluated patterns of phenotypic selection on floral and resistance traits of Gelsemium sempervirens in urban and non-urban sites. The urban landscape had increased florivory and decreased pollen receipt, but showed only modest differences in patterns of selection. Directional selection for one trait, larger floral display size, was stronger in urban compared to non-urban sites. Neither quadratic nor correlational selection significantly differed between urban and non-urban sites. Pollination was associated with selection for larger floral display size in urban compared to non-urban sites, due to differences in the translation of pollination into seeds rather than pollinator selectivity. Thus, our data suggest that urban landscapes may not result in sweeping differences in phenotypic selection but rather modest differences for some traits, potentially mediated by species interactions.
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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
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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.
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