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98 results for “selective pressure”
Dataset for: Expanding risk predictions of pesticide resistance evolution in arthropod pests with a proxy for selection pressure
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Data for: Surviving the serenade: how conflicting selection pressures shape the early stages of sexual signal diversification
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Cryptic sexual dimorphism reveals differing selection pressures on continental islands - Sulawesi Babbler (Pellorneum celebense) Morphometric Dataset
<p>Birds are well known for their sexual dimorphism. But not all forms of dimorphism are the same, and differences in morphology can be so subtle that they aren't detected by casual observation. We report that this is the case with the Sulawesi Babbler (<i>Pellorneum celebense</i>), the first reported instance of sexual dimorphism in this species or any of the ground babblers of the Southeast Asian islands. Our finding is based on a combination of morphometric analyses, genetic sexing, and observation of breeding condition. We highlight the utility of unsupervised clustering approaches, widely used in the biomedical literature, for the investigation of sexual dimorphism in ecological and evolutionary contexts.</p> <p>The sexual dimorphism was weaker on the mainland of Sulawesi and stronger on the continental islands of Kabaena, Muna, and Buton. This suggests that different evolutionary pressures have led the species to partition niches differently in these habitats, which separated only recently in geological history. This kind of intraspecific niche partitioning is an intrinsic part of the ecological niche of such species, one we must not miss if we are to fully understand these endlessly fascinating organisms and systems.</p>
Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
<p>Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.</p>
Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. As shown previously (Souque et al, 2021), the integron can generate under stress combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of <em>P.aeruginosa</em> with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.
Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan
<p>This dataset comprises 43 E gene and 44 complete genome nucleotide sequences of the dengue virus from serotypes DENV-1 to DENV-4, representing all documented sequences in Pakistan to date, sourced from the Virus Pathogen Resource (ViPR) database and NCBI. The E gene is critical as it is involved in serotype changes of the dengue virus, making it a pivotal target for understanding shifts in viral pathogenicity and immune escape mechanisms. The aim of compiling this dataset is to facilitate comprehensive genetic analysis and enhance understanding of the evolutionary dynamics of the dengue virus within the region. To assess the evolutionary pressures acting on these sequences, we conducted a selection pressure analysis utilizing computational methods. These methods include the Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), adaptive Branch Site Random Effects Likelihood (aBSREL), Mixed Effects Model of Evolution (MEME), and the Genetic Algorithm for Recombination Detection (GARD), all implemented in the HyPhy software package. Our analysis focused on identifying genomic sites under both positive and negative selection pressures, providing insights into the adaptive evolutionary processes affecting the E gene of the dengue virus in Pakistan. Understanding the molecular evolution of this gene is crucial for predicting serotype evolution, potentially aiding in the development of effective vaccines and therapeutic strategies.</p>
Data from: Adaptations to climate-mediated selective pressures in humans.
<p>This dataset contains the genotype data in PLINK binary format for the 5 populations genotyped in the Di Rienzo lab and published in </p> <p>Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A (2011) Adaptations to climate-mediated selective pressures in humans. PLoS Genet. 7(4):e1001375</p>
Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures
<p>We here combined evolution experiments with genomic and genetic analyses to assess whether bottleneck size and antibiotic-induced selection influences the evolutionary path to resistance in pathogenic<i> Pseudomonas aeruginosa</i>, one of the most problematic opportunistic human pathogens. Two sets of evolution experiments were performed across 16 transfers, in which either the aminoglycoside gentamicin or the fluoroquinolone ciprofloxacin were used as antibiotic. The evolutionary response was studied using counts of bacterial cells at the end of each transfer period (i.e., yield) or by calculating the growth rate from regular optical density measurement during the respective transfer periods. For the populations at the end of the evolution experiments, we also determined their antibiotic resistance with the help of standardized dose response curves. Moreover, we performed whole genome sequencing to assess the frequency of variants, which emerged and spread during the evolution experiments. We further focused on variants in two specific genes, which were selectively favoured in the gentamicin evolution experiments, and assessed their relative fitness using competition experiments. We found that antibiotic resistance is favoured under high antibiotic selection and weak bottlenecks, but also under low antibiotic selection and severe bottlenecks. We found that the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks in combination with drug-induced selection are currently neglected key determinants of pathogen evolution and antibiotic treatment outcome.</p>
Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard
<p>Hybridization is among the evolutionary mechanisms most frequently hypothesized to drive the success of invasive species, in part because hybrids are common in invasive populations. One explanation for this pattern is that biological invasions coincide with a change in selection pressures that limit hybridization in the native range. To investigate this possibility, we studied the introduction of the brown anole (<i>Anolis sagrei</i>) in the southeastern United States. We find that native populations are highly genetically structured. In contrast, all invasive populations show evidence of hybridization among native-range lineages. Temporal sampling in the invasive range spanning 15 years showed that invasive genetic structure has stabilized, indicating that large-scale contemporary gene flow is limited among invasive populations and that hybrid ancestry is maintained. Additionally, our results are consistent with hybrid persistence in invasive populations resulting from changes in natural selection that occurred during invasion. Specifically, we identify a large-effect X chromosome locus associated with variation in limb length, a well-known adaptive trait in anoles, and show that this locus is often under selection in the native range, but rarely so in the invasive range. Moreover, we find that the effect size of alleles at this locus on limb length is much reduced in hybrids among divergent lineages, consistent with epistatic interactions. Thus, in the native range, epistasis manifested in hybrids can strengthen extrinsic post-mating isolation. Together, our findings show how a change in natural selection can contribute to an increase in hybridization in invasive populations.</p>
Direct Selective Laser Trabeculoplasty (DSLT) for Reducing Eye Pressure in Non-Caucasian Patients With Open Angle Glaucoma
ClinicalTrials.gov study NCT07147647. IPD Sharing: NO. Countries: 1. Publications: 8.
Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures
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Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
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Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard
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Cryptic sexual dimorphism reveals differing selection pressures on continental islands - Sulawesi Babbler (Pellorneum celebense) Morphometric Dataset
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Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan
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A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide
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Noise pollution and artificial light at night alter selection pressures on sexual signals in an urban adapter
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Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
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Data from: Trade-offs between morphology and thermal niches mediate adaptation in response to competing selective pressures
<p>The effects of climate change - such as increased temperature variability and novel predators – rarely happen in isolation, but it is unclear how organisms cope with multiple stressors simultaneously. To explore this, we grew replicate <i>Paramecium caudatum</i> populations in either constant or variable temperatures and exposed half to predation. We then fit thermal performance curves (TPCs) of intrinsic growth rate (<i>r<sub>max</sub></i>) for each replicate population (<i>N</i> = 12) across seven temperatures (10°C - 38°C). TPCs of <i>P. caudatum</i> exposed to both temperature variability and predation responded only to one or the other (but not both), resulting in unpredictable outcomes. These changes in TPCs were accompanied by changes in cell morphology. Although cell volume was conserved across treatments, cells became narrower in response to temperature variability and rounder in response to predation. Our findings suggest that predation and temperature variability produce conflicting pressures on both thermal performance and cell morphology. Lastly, we found a strong correlation between changes in cell morphology and TPC parameters in response to predation, suggesting that responses to opposing selective pressures could be constrained by trade-offs. Our results shed new light on how environmental and ecological pressures interact to elicit changes in characteristics at both the individual and population levels. We further suggest that morphological responses to interactive environmental forces may modulate population-level responses, making prediction of long-term responses to environmental change challenging.</p>
Data from: Wind- and rain-induced vibrations impose different selection pressures on multimodal signaling
The world is a noisy place, and animals have evolved a myriad of strategies to communicate in it. Animal communication signals are, however, often multimodal; their components can be processed by multiple sensory systems, and noise can thus affect signal components across different modalities. We studied the effect of environmental noise on multimodal communication in the túngara frog (Physalaemus pustulosus). Males communicate with rivals using airborne sounds combined with call-induced water ripples. We tested males under control as well as noisy conditions in which we mimicked rain- and wind-induced vibrations on the water surface. Males responded more strongly to a multimodal playback in which sound and ripples were combined, compared to a unimodal sound-only playback, but only in the absence of rain and wind. Under windy conditions, males decreased their response to the multimodal playback, suggesting that wind noise interferes with the detection of rival ripples. Under rainy conditions, males increased their response, irrespective of signal playback, suggesting that different noise sources can have different impacts on communication. Our findings show that noise in an additional sensory channel can affect multimodal signal perception and thereby drive signal evolution, but not always in the expected direction.
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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.