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95 results for “stabilizing selection”
Overcoming Limitation of AlphaFold2 by Deep-mutational Scanning and Stability-Selection of Protein Sequences
<p>This repository contains the processed datasets and corresponding code used in our study. While AlphaFold2 revolutionizes protein structure prediction, its accuracy critically depends on evolutionary information from natural homologs—limiting applications for proteins with sparse sequence families. Here, we bypass this bottleneck by employing deep mutational scanning and stability-guided selection to generate artificial homologs. Fed into AlphaFold2, these synthetic sequences match the accuracy achieved on well-predicted proteins with rich natural homology, while providing highly accurate predictions for difficult targets—including orphan proteins previously deemed "unpredictable." Our approach achieves high accuracy (<3 Å RMSD for 5/8 and <2 Å RMSD for 7/8 targets after excluding intrinsically flexible regions). Thus, integrating simple, scalable molecular biology (mutagenesis/selection) with high-throughput sequencing can deliver the accuracy similar to but at a fraction of the cost and time of traditional experimental structure-determination methods. This hybrid framework could democratize high-resolution structural biology, opening avenues to determine structures of protein complexes, modified proteins, and condition-dependent conformations. </p>
Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption (increasing trait variation and potentially generating new traits) or stabilization (decreasing trait variation). In the short term, stabilization is more economical, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalization is deleterious in the face of persistently increasing stress, because it reduces variability and thus decreases the ability to react to further changes. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptation of populations facing extinction are rare. Here, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variation in two species across a salinity rise leading to their local extinction. One species reacted by stabilization in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remained stable or reacted by further stabilization. These observations indicate that the default reaction of the studied Foraminifera is canalization, and that stress escalation did not lead to the emergence of adapted forms. An inherent inability to breach the global adaptive threshold would explain why communities of Foraminifera and other marine protists reacted to Quaternary climate change by tracking their zonally shifting environments. It also means that populations of marine plankton species adapted to response by migration will be at risk of extinction when exposed to stress outside of the adaptive range.
Metadata of " Stability of Selected Hydrogen Bonded Semiconductors in Organic Electronic Devices"
<p>Metadata of " Stability of Selected Hydrogen Bonded Semiconductors in Organic Electronic Devices"</p>
Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
Open the record for dataset details and reuse information.
Stabilizing selection on a plumage-based foraging adaptation: hooded warblers with average-sized white tail spots live longer
<p><span>Avian flush-pursuit insectivores typically use contrasting white plumage patches in their tails or wings to startle potential prey. Although experimental evidence indicates that the extent of white has been fine-tuned by natural selection to optimize foraging performance, the hypothesis that within-population plumage variation directly influences survival or lifetime reproduction and is subject to stabilizing selection has not been tested. Here I provide such a test using data collected as part of a 14-year study of a colour-ringed breeding population of the hooded warbler (<em>Setophaga</em> <em>citrina</em>), a migratory flush-pursuit insectivore that shows inter-individual variation in the extent of white in the tail that is highly repeatable across molts and likely heritable. As expected under stabilizing selection, warblers with average-sized white tail patches achieved significantly higher long-term apparent survival than individuals with either a lesser or greater extent of white in the tail. Evidence of stabilizing selection was especially strong in males, an observation that is likely related to pronounced sexual habitat segregation on the wintering range. My results provide infrequently observed evidence of stabilizing selection operating in a natural population and also illustrate how stabilizing selection can act on avian plumage traits outside the context of sexual and social signaling.</span></p>
Figure 9 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 9. Five sequential matings (1-2, 3, 4, 5-6, 7) of the two male forms with the same female Maevia inclemens over the course of five days. 1-2, This mating was interrupted as the male switched from one side to the other, but after an atypical low crawl display with legs I extended, the tufted male quickly recaptured the female and continued to mate on the other side. 5-6, mating on the right and then left sides. Note the many erect spines on the legs of the mating male in each instance.
Figure 8 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 8. Sequential positions (1-4) of the tufted male Maevia inclemens as he advanced toward the female in a still later mating attempt (after Figure 7). Here the view of the female is shown. 1-2, Waving legs I. 3, Fully extended for maximum height. 4, Display from a lower position with raised legs I.
Figure 3 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 3. Adult male Maevia inclemens, tufted (black) form. The tufts of the dorsal carapace may not be present in all males of this form. Note the lack of stripes on the uniformly-colored legs. 2, Feeding on mosquito (Diptera: Culicidae).
Figure 4 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 4. Four sequential positions of a male (1-4) during the successful courtship of a female Paraphidippus aurantius (Lucas 1833) on a plant in the laboratory. Males were placed on plants with three recently molted females, all from Greenville County, South Carolina. In each case the female stopped moving soon after she sighted the male, and the male advanced to mate successfully when she did not turn to face him as he stepped from side to side. In this example the female stopped moving at a distance of about 10 cm from the approaching male. The subsequent mating included insertion of each pedipalp on the respective side of the epigynum, and occupied more than 20 minutes. P. aurantius males will cohabit with and defend penultimate females (Thurlow 2016), and their large chelicerae are associated with the ritual male-male combat (agonistic behavior) that may ensue. This represents a pattern seen in many other salticids (e.g., Lyssomanes viridis, Tedore & Johnsen 2012, 2013, 2015), in which male-male contests account for most sexual selection. At the other end of the spectrum of sexual selection lie the highly ornamented salticids of the genus Maratus, for which male-male contests are virtually unknown (save one species), and a female may examine the details of male ornamentation up-close before acceptance (Otto & Hill 2021). Most salticids appear to fall somewhere between these two extremes, relying to some extent on both male-male combat and active selection by females.
Figure 1. Adult female Maevia inclemens. 1-2, 6 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 1. Adult female Maevia inclemens. 1-2, 6, Feeding on a small fly (Diptera: Brachycera). 3-4, Feeding on a small robber fly (Diptera: Ascilidae). With the exception of Figure 5:8, only three M. inclemens individuals, two males and one female, all photographed on plants in the laboratory, are shown in this paper. All were collected in Massachusetts, June 2020.
Figure 7 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 7. Sequential positions (1-10) of the tufted male Maevia inclemens as he advanced toward the female in a later mating attempt (after Figure 6).
Figure 10 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 10. Attempted mating by the grey male Maevia inclemens. This sequence shows how the male jumped the female while she was suspended from her dragline, just after capturing a fly (1), and attempted to mate with her (2). The female promptly released her prey, and the male then fed on it for many minutes (3-4), still in a suspended position [23 JUNE 2020 14:09- 14:13]. Three days later this male approached and mated successfully with the female for a second time (Figures 5:1-7, 9:7).
Figure 5 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 5. Display by grey males, Maevia inclemens. 1-7, Successive (low crawl) positions of the grey male male from Massachusetts, advancing to successfully mate with the female. When close, this male jumped and captured the female (Figure 9:7). 8, Display by a grey male from Sherburne County, Minnesota, recorded in 1982.
Figure 2 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 2. Adult male Maevia inclemens, grey (striped) form. Note the stripes on the prolateral surface of each femur.
Figure 11 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)
Figure 11. Sequential (1-2) views of encounter between the two male forms of Maevia inclemens. Apart from a brief defensive reaction by the grey male (2), no ritual combat ensued and the males did not appear to recognize that they were conspecific.
An Evaluation of the Hydrolytic Stability of Selected Experimental Dental Matrices and Composites
<p>Materials with potential use as dental restoration should be evaluated in an aggressive environment. Such accelerated aging is widely used in other industries and allows the assessment of service life. In the presented study, three neat resins (UDMA/Bis-GMA/TEGDMA 70/10/20 wt.%, UDMA/Bis-GMA/TEGDMA 40/40/20 wt.% and UDMA/Bis-EMA/TEGDMA 40/40/20 wt.%) and three composites based on these matrices were tested before and after aging protocols (I-7500 cycles, 5 °C and 55 °C, water and 7 days, 60 °C, 0.1 M NaOH; II-5 days, 55 °C, water and 7 days, 60 °C, 0.1 M NaOH). Flexural strength (FS), diametral tensile strength (DTS) and hardness (HV) were determined. Applied aging protocols resulted in a decrease in the value of the FS, DTS and HV. Larger changes were noticed for the neat resins. Materials in which the content of bis-GMA was lower or substituted by bis-EMA showed better resistance to degradation. The choice of mixtures with monomers characterized by lower sorption values may favorably affect hydrolytic stability. It was shown that for composites there was a drastic decrease in hardness, which suggests a more superficial effect of the used protocols. However, degradation of the surface layer can result in a growing problem over time given that the mastication processes are an inherent element in the oral environment.</p> <p> </p>
Open data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters
<p>Original data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters, published in Small, 2023.</p> <p>The dataset is organized according to the Figures in the manuscript.</p>
Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis
<p>Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remains unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., QST-FST comparisons). A redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a QST-FST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of S. canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Does natural selection drive phenotypic trait variation among S. canadensis populations? (2) Do climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., QST >FST) and stabilizing selection for physiological traits (i.e., QST < FST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. Precipitation seasonality that was associated with longitudinal shift in China likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped phenotypic traits of S. canadensis.</p>
Figure 11 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 11. Sequential (1-2) views of encounter between the two male forms of Maevia inclemens. Apart from a brief defensive reaction by the grey male (2), no ritual combat ensued and the males did not appear to recognize that they were conspecific.
Figure 9 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 9. Five sequential matings (1-2, 3, 4, 5-6, 7) of the two male forms with the same female Maevia inclemens over the course of five days. 1-2, This mating was interrupted as the male switched from one side to the other, but after an atypical low crawl display with legs I extended, the tufted male quickly recaptured the female and continued to mate on the other side. 5-6, mating on the right and then left sides. Note the many erect spines on the legs of the mating male in each instance.
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