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1,812 results for “dissection”
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
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Data from: Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins
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Data from: Dissecting the genetic architecture of a stepwise infection process
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Data from: Dissecting abstract, modality-specific and experience-dependent coding of affect in the human brain
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Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
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Link to dataset related to article "Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells"
<p>Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of <em>cis</em>-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated <em>cis</em>-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.</p>
Dissection for floral micromorphology and plastid genome of valuable medicinal borages Arnebia and Lithospermum (Boraginaceae)
<p>The genera <em>Arnebia </em>and <em>Lithospermum </em>(Lithospermeae-Boraginaceae) comprise 25–30 and 50–60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots of <em>Arnebia euchroma</em>, <em>A. guttata</em>, and <em>Lithospermum erythrorhizon</em>, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences of <em>A. guttata </em>(including <em>A. tibetana</em>), <em>A. euchroma</em>, and <em>L. erythrorhizon</em>. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361–150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (<em>atpH-atpI, petN-psbM, rbcL-psaI, ycf4-cemA, ndhF-rpl32, </em>and <em>ndhC-trnV-UAC</em>). To facilitate species identification, we developed molecular markers <em>psaA- ycf3 </em>(PSY), <em>trnI-CAU- ycf2 </em>(TCY), and <em>ndhC-trnV-UAC</em> (NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship of <em>Arnebia </em>to its <em>Lithospermum </em>sister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest that <em>A. tibetana</em>, might be recognized as an independent species rather than a synonym of <em>A. guttata</em>. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.</p>
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup
<p>Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.</p>
Data from: Dissecting biodiversity in a global hotspot: uneven dynamics of immigration and diversification within the Cape Floristic Region of South Africa
Aim: Fragmented distributions should show immigration and diversification dynamics consistent with the predictions of island biogeography theory. We test whether this applies to the fragmented Cape fynbos vegetation. Location: Southern Africa, Cape Floristic Region (CFR) Taxon: Angiosperms, Restionaceae (restios) Methods: We used a large occurrence dataset and environmental layers to characterize an existing regionalization and the intervals between the regions ecologically and spatially. We extended the available phylogeny for restios and inferred their historical biogeography using models implemented in BioGeoBEARS. We then measured the relative contribution of immigration and in situ speciation to the species richness of each region within the CFR. We used standard statistical methods to test the predictions of the island biogeography theory. Results: The area and environmental heterogeneity of the seven regions of the CFR are positively correlated with in situ speciation rate. Furthermore, more isolated areas, and areas colonized more recently, have proportionally higher immigration rates, and more central and older areas proportionally higher in situ speciation rates. Main Conclusions: The variation in immigration and diversification dynamics among the regions within the CFR is extensive and consistent with the archipelago model of island biography theory. This dynamic may contribute significantly to the diversity of the Cape flora. Such a model could be generally useful for understanding the generation and maintenance of diversity in biodiversity hotspots, and may even scale up to explain continental biodiversity.
Data from: Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population
Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade-off between them, either at the phenotypic or genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker-based approaches - chromosome partitioning, quantitative trait locus (QTL) mapping and a genome-wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome-wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, non-significant, negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.
Data from: Anatomy of a cline: dissecting anti-predatory adaptations in a marine gastropod along the U.S. Atlantic coast
The scope of anti-predatory adaptation is expected to be greater in warm than in cold environments. High temperatures lower the costs associated with the production and maintenance of energetically expensive traits and enable ecological interactions to intensify. We tested this hypothesis by characterizing the expression of anti-predatory morphology within a marine gastropod species (the knobbed whelk, Busycon carica) over a large (>1,400 km) geographic area that spans more than 10°C annual temperature variation. We also conducted experimental predation studies with a powerful durophagous predator, the stone crab (Menippe), to verify the anti-predatory advantages of a heavily ornamented shell morphology (e.g., increased thickness, pronounced spines), and we used repair scar data to assess clinal variation in selective pressure from predators. We predicted that repair scar rates would be greatest in warm southernmost latitudes, and that expression of energetically costly anti-predatory morphology would peak in concert with elevated predation pressures. Experiments confirmed that whelks with energetically costly, heavily ornamented shells had higher survivorship rates than those with weakly ornamented shells. As predicted, we also found that the expression of anti-predatory traits was greatest in the southern part of B. carica's range. After standardizing shells for size, shape, and exposure time to enemies, repair scar rates also peaked to the south. Taken together, these results suggest that the expression of anti-predatory traits along the geographic cline is governed by the interaction of two selective factors: temperature and predation, with the former acting as the ultimate control on the scope of adaptation both by escalating predation pressure in the southern part of B. carica's range and by physically limiting (to the north) and facilitating (to the south) the production of anti-predatory traits. Feedbacks between temperature and predation thus causally interact to enable and drive, respectively, the observed geographic cline in energy-intensive anti-predatory shell traits.
Data from: Canopy leaf area index at its higher end: dissection of structural controls from leaf to canopy scales in bryophytes
There is evidence that mosses with miniature foliage elements have extremely large leaf area indices (LAI), but it is unclear what canopy traits are responsible for these high LAI values in architecturally divergent mosses, and how the inherent tradeoffs limiting maximum LAI in vascular plants can be overcome in mosses. To determine the quantitative significance of different traits in determining LAI, we developed a method to dissect LAI into underlying functionally dependent constituent traits at leaf, shoot and canopy scales. The suites of structural traits were studied altogether for 43 moss canopies from 11 species with contrasting light and water requirements along gap-understory gradients to obtain as large a range of variation in moss architecture as possible and evaluate the differentiation in moss LAI in relation to species ecology. Extensive variation in moss structural traits, 11- (shoot length) to 77-fold (shoot number per area, NS), was observed at all structural scales from leaf to canopy. However, LAI only varied 9-fold, as the result of two key tradeoffs, leaf size vs. number tradeoff and shoot leaf area vs. shoot density tradeoff. Due to these negative relationships, and greater variability in NS, LAI primarily scaled with NS. and LAI increased with site light availability, and LAI was greater in open and dry habitat species. The current study highlights a huge structural diversity among moss canopies, but indicates that canopies converge to a much narrower range of LAI due to trait tradeoffs such that, counterintuitively, minute leaf size and densely leafed stems are not necessarily responsible for high LAI in mosses.
Data from: Dissecting the hydrological niche: soil moisture, space and lifespan
Questions: Are communities structured on a hydrological (soil moisture) gradient? Is there spatial segregation into hydrological niches? What is the shape of the hydrological niches of individual species? Controlling for spatial autocorrelation, how much of the spatial structure in the community is due to variation in hydrology? Do annuals and perennials behave alike with respect to the above questions? Locations: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the Urbión Peaks, Soria, central-northern Spain (alpine grassland). Methods: The presence of plant species was sampled in two contrasting field sites, for which we also built hydrological models. First, we reduced the dimensionality of the plant distribution data (non-metric multidimensional scaling) and measured the correlation between the resulting ordination and the hydrological gradient. Then we defined hydrological niches and tested niche segregation of plant species against null models (Pianka metrics). Finally, we characterized the hydrological niche of each species using generalised additive mixed models and partitioned the species distribution variance into (1) a hydrological component, (2) a linear trend component and (3) and a spatial component, defined through sets of spatial variables (Moran's eigenvector maps). Results: Both plant communities were primarily structured along hydrological gradients, and spatial segregation into hydrological niches occurred among perennial species, although not among annuals in the dehesa community. Dehesa annuals were spatially aggregated in the driest niches. Hydrological variation shaped the responses of 60% of the annual and about 70% of the perennial species in both the dehesa meadow and the alpine community. Most responses were either monotonic or hump-shaped. Finally, spatially structured hydrological variation proved to be the main driver of spatially structured species composition in all cases. Conclusions: Linearly (gradient of slope) and topographically (at a fine scale) structured variation in hydrology is the main driver of spatially structured species composition in both communities. Our results support the ecological hypothesis that spatial niche segregation on soil moisture gradients is an important mechanism of co-existence for perennials in both test communities, although not for the species-rich sub-community of annuals in the dehesa meadow.
Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing
Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
Data from: Dissecting nutrient-related co-expression networks in phosphate starved poplars
Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation. These genes clustered in eleven co-expression modules of which seven were correlated with distinct elements in the plant tissues. One module (4.7% of all differentially expressed genes) was strongly correlated with changes in the P concentration in the plant. In this module the GO term "response to P starvation" was enriched with phosphoenolpyruvate carboxylase kinases, phosphatases and pyrophosphatases as well as regulatory domains such as SPX, but no phosphate transporters. The P-related module was also enriched in genes of the functional category "galactolipid synthesis". Galactolipids substitute phospholipids in membranes under P limitation. Two modules, one correlated with C and N and the other with biomass, S and Mg, were connected with the P-related module by co-expression. In these modules GO terms indicating "DNA modification" and "cell division" as well as "defense" and "RNA modification" and "signaling" were enriched; they contained phosphate transporters. Bark storage proteins were among the most strongly upregulated genes in the growth-related module suggesting that N, which could not be used for growth, accumulated in typical storage compounds. In conclusion, weighted gene coexpression network analysis revealed a hierarchical structure of gene clusters, which separated phosphate starvation responses correlated with P tissue concentrations from other gene modules, which most likely represented transcriptional adjustments related to down-stream nutritional changes and stress.
Data from: Genetic dissection of hybrid male sterility across stages of spermatogenesis
Hybrid sterility is a common form of reproductive isolation between nascent species. Although hybrid sterility is routinely documented and genetically dissected in speciation studies, its developmental basis is rarely examined, especially in generations beyond the F1. To identify phenotypic and genetic determinants of hybrid male sterility from a developmental perspective, we characterized testis histology in 312 F2 hybrids generated by intercrossing inbred strains of Mus musculus domesticus and M. m. musculus, two subspecies of house mice. Hybrids display a range of histologic abnormalities that indicate defective spermatogenesis. Among these abnormalities, we quantified decreased testis size, reductions in spermatocyte and spermatid number, increased apoptosis of meiosis I spermatocytes, and more multinucleated syncytia. Collectively, our phenotypic data point to defects in meiosis I as a primary barrier to reproduction. We identified seven quantitative trait loci (QTL) controlling five histologic traits. A region of chromosome 17 that contains Prdm9, a gene known to confer F1 hybrid male sterility, affects multinucleated syncytia and round spermatids, potentially extending the phenotypic outcomes of this incompatibility. The X chromosome also plays a key role, with loci affecting multinucleated syncytia, apoptosis of round spermatids, and round spermatid numbers. We detected an epistatic interaction between QTL on chromosomes 17 and X for multinucleated syncytia. Our results refine the developmental basis of a key reproductive barrier in a classic model system for speciation genetics.
Data from: Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance
Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed "hemiplasy"—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and to introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.
Data from: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms. Here we studied patterns of reproductive isolation among three taxa, An. coluzzii, An. gambiae s.s. and An. arabiensis, to compare its strength at different spatial scales, to dissect the relative contribution of pre- versus post-mating isolation, and to infer the involvement of ecological divergence on hybridization. Because F1 hybrids are viable, fertile, and not uncommon, understanding the dynamics of hybridization in this trio of major malaria vectors has important implications for how adaptations arise and spread across the group, and in planning studies of the safety and efficacy of gene drive as a means of malaria control. We first performed a systematic review and meta-analysis of published surveys reporting on hybrid prevalence, showing strong reproductive isolation at a continental scale despite geographically restricted exceptions. Second, we exploited our own extensive field datasets collected at a regional scale in two contrasting environmental settings, in order to assess: i) levels of pre-mating isolation; ii) spatio/temporal and frequency-dependent dynamics of hybridization, iii) relationship between reproductive isolation and ecological divergence, and iv) hybrid viability penalty. Results are in accordance with ecological speciation theory predicting a positive association between the strength of reproductive isolation and degree ecological divergence, and indicate that post-mating isolation does contribute to reproductive isolation among these species. Specifically, only post-mating isolation was positively associated with ecological divergence, whereas pre-mating isolation was correlated with phylogenetic distance.
Data from: Dissecting the variation of a visual trait: the proximate basis of UV-Visible reflectance in crab spiders (Thomisidae)
1. The astounding diversity of animal colouration is indicative of a wide variety of selection pressures. Despite great interest in adaptive function, detailed understanding of the constituent elements of colour traits is lacking for many systems. Such information is important in allowing more accurate appraisals of colour variation and its potential production costs. 2. In this study, we 'dissect' the dorsal colour of crab spiders (Thomisidae) to examine the mechanistic basis of a polyphenic colour trait. These spiders possess the ability to alter reflectance in the ultraviolet (UV), violet and blue wavelengths, changing their colour within days. We investigate and compare the proximate mechanistic basis of colour production in multiple phenotypes of three species using histology and spectrophotometry. 3. Our analyses indicate that the spider cuticle is not equivalently transparent to light across the spectrum (300-700 nm) – as previously argued – and contributes to colour variation. UV light is reflected from guanine crystals, present in storage cells ventral to the hypodermis. The crystals are exposed through a partially UV-transmitting hypodermis and cuticle. Variation from white to yellow is likely mediated through pigments/crystals present in different oxidative stages in the hypodermal cells. 4. Simple mechanistic changes are therefore necessary to produce the observed variation, and likely underlie the evolutionary and ontogenetic lability of this trait. Our findings imply that either a UV-reflective abdomen was the ancestral state for crab spiders, or, if pre-dated by UV-absorbent hypodermal pigments, the evolution of UV-reflection has only involved the exposure of underlying guanine crystals through an otherwise clear hypodermis.
FIGURE 1. Bathytanais culterformis, female. A holotype, BL dissected paratype. A in A new tanaidacean subfamily, Bathytanaidinae (Crustacea: Paratanaididae), from the Australian continental shelf and slope
FIGURE 1. Bathytanais culterformis, female. A holotype, BL dissected paratype. A) Dorsal view. B) Cephalothorax. C) Antennule. D) Antenna. E) Labrum. F) Left mandible. G) Right mandible. H) Labium. I) Maxillule and maxilla. J) Maxilliped. K) Epignath. L) Cheliped.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.