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4,480 results for “hybrid”
Quantum efficiency and vertical position of quantum emitters in hBN determined by Purcell effect in hybrid metal-dielectric planar photonic structures
<p>Data from the article "Quantum efficiency and vertical position of quantum emitters in hBN determined by Purcell effect in hybrid metal-dielectric planar photonic structures", <a href="https://pubs.acs.org/doi/10.1021/acsphotonics.4c01416">ACS Photonics, (2024)</a> - [arXiv:2407.20160]</p>
THE HYBRID HISTORY OF ZEBRAFISH
<p>This repository contains files associated with the manuscript titled "The Hybrid History of Zebrafish" by <span><span>Braedan M.</span> <span>McCluskey</span></span>, <span><span>Peter</span> <span>Batzel</span></span>, and<span><a href="http://orcid.org/0000-0002-5476-2137" target="_blank" rel="noopener"> </a><span>John H.</span> <span>Postlethwait. <br><br></span></span>In addition to code used during the analysis, this repository contains the multiple sequence alignment used for phylogenetic inference (geno.phy), the resulting phylogeny inferred by RAxML (RAxML_bipartitionsBranchLabels.geno), the genotypes called for each species (geno.vcf.gz), and the genotypes called for 12 zebrafish samples from previous studies (DrerioRAD_12Samples.vcf.gz). </p>
Replication Package: Block-based or Graph-Based? Why Not Both? Designing a Hybrid Programming Environment for End-users
<p><strong>Block-based or Graph-based? Why Not Both? Designing a Hybrid Programming Environment for End-users: Replication Package</strong></p> <p>This repository contains supplementary materials for the paper "Block-based or Graph-based? Why Not Both? Designing a Hybrid Programming Environment for End-users". We provide this data for transparency reasons and to support replications of our experiments.</p> <p><strong>Summary of files contained in this package</strong></p> <p>This package contains two parts:</p> <ul> <li> <p>The <code>data-analysis/</code> folder contains the raw dataset we collected for our experiment in CSV format, as well as scripts we used for our analyses.</p> <ul> <li>Column <code>ID</code> contains a unique 4-digit identifier for each participant that they were assigned throughout our study.</li> <li>Column <code>Group</code> contains the group (Blocks/Graph) that participants were randomly assigned to.</li> <li>Columns <code>Task1Time</code> and <code>Task2Time</code> contain the time participants spent to complete the two programming tasks of our study in minutes.</li> <li>Columns <code>Task1Success</code> and <code>Task2Success</code> contain a boolean value indicating whether the participants successfully completed the given task. Note that participants had unlimited attempts until they timed out after a strict time limit of 30 minutes, so if a participant was unsuccessful the corresponding time value is 30.</li> <li>Columns <code>Task1Tests</code> and <code>Task2Tests</code> contain the number of times a participant executed their code throughout a task, including their final submission if they were successful.</li> <li>Columns <code>LearnTask</code>, <code>ReadTask</code> and <code>WriteTask</code> contain the scores that participants gave to the task editor component of their assigned programming environment. There are 3 scores for the categories "learnability", "readability" and "writability". Scores are on a 5-point scale from 1 (worst) to 5 (best).</li> <li>Columns <code>LearnTrig</code>, <code>ReadTrig</code> and <code>WriteTrig</code> contain the scores that participants gave to the trigger editor component of their assigned programming environment. There are 3 scores for the categories "learnability", "readability" and "writability". Scores are on a 5-point scale from 1 (worst) to 5 (best).</li> <li>Columns <code>LearnComp</code>, <code>ReadComp</code> and <code>WriteComp</code> contain the scores that participants gave to their assigned assigned programming environment in direct comparison to the other alternative. There are 3 scores for the categories "learnability", "readability" and "writability". Unlike in the paper, where scores are on a scale from -2 to 2, the raw scores here are on a 5-point scale from 1 (strong preference for other environment) to 5 (strong preference for own environment).</li> <li>The script <code>successplot.py</code> was used to generate the success rate plot used in a figure in the paper</li> <li>The script <code>survival.py</code> was used to perform the survival analysis presented in the paper and generate the related figure.</li> <li>The script <code>batplot.py</code> was used to generate the 3x3 grid of ratings used in a figure in the paper.</li> </ul> </li> <li> <p>The <code>materials/</code> folder contains the tutorials and task descriptions we presented to study participants. It also contains the exact wording of pre-screening and post-experiemental survey questions.</p> <ul> <li>The image <code>pre-screening.png</code> shows the three pre-screening questions we used to determine whether our participants could be included in our study.</li> <li>The images <code>tutorial1_instructions.png</code> and <code>tutorial1_sim.png</code> contain the instructions and initial simulator state we provided to participants for the first programming tutorial. This tutorial did not provide starter code and was identical for both participant groups.</li> <li>The images <code>tutorial2_instructions.png</code> and <code>tutorial2_sim.png</code> contain the instructions and initial simulator state we provided to participants for the second programming tutorial. This tutorial was identical for both participant groups and provided participants with starter code, which is shown in the images: <ul> <li><code>tutorial2_code_main.png</code> for the main program in the left canvas</li> <li><code>tutorial2_code_move.png</code> for the definition of "Move box to the right".</li> </ul> </li> <li>The images <code>tutorial3_instructions_blocks.png</code>/<code>tutorial3_instructions_graph.png</code> and <code>tutorial3_sim.png</code> contain the instructions and initial simulator state we provided to participants for the third programming tutorial. This tutorial also provided participants with starter code, which is shown in the images: <ul> <li><code>tutorial3_code_main.png</code> for the main program in the left canvas</li> <li><code>tutorial3_code_pick.png</code> for the definition of "Pick up box"</li> <li><code>tutorial3_code_place.png</code> for the definition of "Place box"</li> </ul> </li> <li>The images <code>task1_instructions.png</code> and <code>task1_sim.png</code> contain the instructions and initial simulator state we provided to participants for the first programming task. The task did not provide starter code and the instructions were identical for both participant groups.</li> <li>The images <code>task2_instructions.png</code> and <code>task2_sim.png</code> contain the instructions and initial simulator state we provided to participants for the second programming task. The instructions were identical for both groups. This task also provided participants with starter code, which is shown in the images: <ul> <li><code>task2_code_main.png</code> for the main program in the left canvas</li> <li><code>task2_code_pick_prog.png</code> for the definition of "Pick up block"</li> <li><code>task2_code_load_trig_blocks.png</code>/<code>task2_code_load_trig_graph.png</code> for the definition of the trigger "Ready to load machine"</li> <li><code>task2_code_load_prog.png</code> for the definition of "Load and activate machine"</li> <li><code>task2_code_finished_trig_blocks.png</code>/<code>task2_code_finished_trig_graph.png</code> for the definition of the trigger "Machine finished"</li> <li><code>task2_code_finished_prog1.png</code> for the definition of "Get block from machine"</li> <li><code>task2_code_finished_prog2.png</code> for the definition of "Place block in bin"</li> </ul> </li> <li> <div>The document <code>post_survey_full.pdf</code> contains a raw export of the comprehension questions and post-experimental survey as they were presented to participants </div> </li> <li>The image <code>usability.png</code> shows the usability questions we used to determine a participant's rating of their assigned programming environment. The questions were identical for both participant groups.</li> <li>The images <code>comprehension_blocks_1.png</code> and <code>comprehension_blocks_2.png</code> show the program comprehension questions we used to determine whether participants in the Blocks group could understand more complex triggers.</li> <li>The images <code>comprehension_graph_1.png</code> and <code>comprehension_graph_2.png</code> show the program comprehension questions we used to determine whether participants in the Graph group could understand more complex triggers.</li> <li>The images <code>comparison_blocks.png</code> and <code>comparison_graph.png</code> show the images of triggers in the alternative environment that we showed to our participants before choosing their preferred environment. The questions were identical for both participant groups.</li> <li>The image <code>comparison.png</code> shows the questions we used to determine a participant's preference between the two programming environment alternatives.</li> </ul> </li> </ul>
Replication package for "An Empirical Evaluation of Static, Dynamic, and Hybrid Slicing of WebAssembly Binaries"
<p>This is the replication package that accompanies the paper "An Empirical Evaluation of Static, Dynamic, and Hybrid Slicing of WebAssembly Binaries".</p> <p>It is structured as follows.</p> <p> - RQs.py is the script that generates the data that is included in the paper. For each research question, it generates statistics and plots.<br> - The .csv files and nok.txt are used by RQs.py. They contain the raw size and timing data for each slice. The headers of the .csv files indicate what each column represents.<br> - `sqlite-slices.csv` contains the raw data for RQ8, which is contained in the paper<br> - The .tar.gz files contain the source and the slices generated by each slicer, namely:<br> - `static_slices.tar.gz` contains the slices generated by CsE, the static slicer. For example, the file `static_slices/adpcm/adpcm_ah1_254_expr/static_adpcm.wat.slice` is the slice of the adpcm program taken with respect to the variable `ah1` at line `254` of the original `.c` program.<br> - `slice.tar.gz` contains slices from the dynamic slicers:<br> - slice-sce - the SCE slices<br> - slice-ces - the CES slices<br> - slice-cse - the CSE slices<br> - slice-sces - the SCES slices<br> - slice-cses - the CsES slices<br> - `src.tar.gz` includes the unsliced `C` and `wasm` source<br> - `bc.support.tar.gz` includes the complete `bc` source code <br> - `sqlite.tar.gz` contains the slices of RQ8, each in a directory named after the slicer used. For example, the file `sqlite/CES/avg.wat` contains the CES slice for the `avg` slicing criterion.<br> <br>In order to regenerate the data and plots that are in the paper, you should simply run:</p> <p>```<br>python RQs.py<br>```</p>
Data from: Invasive hybridization has variable effects on survival among salmonid populations
<p>Human-mediated hybridization threatens global biodiversity, but the fitness consequences of hybridization are poorly understood, especially in vertebrates. We used capture-recapture data from 5,249 individuals in three hybridizing populations of invasive rainbow trout (<i>Oncorhynchus mykiss</i>) and native cutthroat trout (<i>O. clarkii</i>) to quantify the effects of rainbow trout genetic admixture and environmental conditions on survival. Seasonal variation in environmental conditions interacted with individual admixture to influence seasonal survival. Overall, annual survival declined with admixture at the warmest site (juvenile hybrids with 25% non-native ancestry had 20.7% lower annual survival than non-hybridized cutthroat trout) but increased with admixture at the coldest site (juvenile hybrids with 25% non-native ancestry had 19.7% higher survival than non-hybridized cutthroat trout), providing evidence that fitness effects of hybridization vary in a context-dependent manner. Furthermore, higher survival for hybrids in cold streams and lower survival in warm streams is opposite of admixture-environment correlations, demonstrating that environmental gradients often used to infer patterns of hybridization may poorly predict variation in fitness across the landscape.</p> <p>Individual-based studies measuring fitness-related traits in vertebrate taxon are rare. Most studies of human-mediated hybridization in wild populations quantify the spatial extent of non-native admixture or test for admixture-environment associations to infer factors affecting fitness in hybridizing populations. We used an extensive capture-recapture dataset to measure seasonal survival in hybridized populations that experience different environmental conditions. Our work shows that non-native admixture can affect survival differently among seasons and populations, and that inferences from individual-based studies can conflict with those from admixture-environment associations. For studies of non-native hybridization, this work highlights the importance of directly measuring fitness (survival and reproductive success), and at appropriate spatial and temporal scales to elucidate the variation in fitness differences (i.e., among populations and seasons).</p>
Data From: Fit and fatty freshwater fish: Contrasting polyunsaturated fatty acid phenotypes between hybridizing stickleback lineages
<p>Long-chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales of evolutionary divergence: between two lineages with different metabolic capacities for fatty acid synthesis (i.e. different copy number of the fatty acid desaturase gene; FADS2) that independently colonized European freshwaters during the Pleistocene and Holocene; and between two ecotypes within each lineage that have diverged more recently (~150 years) in different habitats (i.e. lake and stream). We measured fatty acid profiles of wild-caught and lab-reared fish for each lineage and ecotype combination after rearing lab fish on a diet deficient in omega-3 long-chain polyunsaturated fatty acids. Since these lineages hybridize in nature, we also measured profiles of lab-reared hybrids and backcrosses raised on the same deficient diet. Wild fish showed strong compositional differences in fatty acids between habitats, lineages, and sexes. Common garden fish had generally lower polyunsaturated fatty acid levels than wild fish, and females had lower omega-6:omega-3 than males. Fish from the lineage with fewer FADS2 copies also had lower levels of docosahexaenoic acid. Overall, we document divergence in fatty acid phenotypes between stickleback lineages with different histories of freshwater colonization, and between ecotypes in the early stages of adaptive population divergence.</p>
Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridization capture
<p>This dataset complements a manuscript reporting genomic analyses of respiratory pathogens cuasing lethal outbreaks in the wild chimpanzee community living in Tai National Park, Ivory Coast.</p>
Pictures of Kombar barley infected with Pyrenophora teres f. teres and Pyrenophora teres f. maculata pure and hybrid progeny isolates
<p>Progeny isolates from three bi-parental Pyrenophora teres populations were inoculated on Kombar barley and their 7dpi reaction type was photographed. The populations used included two pure crosses, P. teres f. teres and P. teres f. maculata isolates crossed to other isolates of the same P. teres form and one hybrid cross generated by crossing P. teres f. teres and P. teres f. maculata isolates. The P. teres f. teres pure cross was 15Ax0-1, the P. teres f. maculata pure cross was FGOB10Ptm-1xSG1, and the hybrid cross was FGOB10Ptm-1x0-1. </p>
Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome
<p>Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a></p>
Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones
<p><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">The</span><span class="NormalTextRun SCXW104780834 BCX0"> process of species formation is </span><span class="NormalTextRun SCXW104780834 BCX0">characterised by the accumulation</span><span class="NormalTextRun SCXW104780834 BCX0"> of </span><span class="NormalTextRun SCXW104780834 BCX0">multiple reproductive barriers. The evolution</span><span class="NormalTextRun SCXW104780834 BCX0"> of </span><span class="NormalTextRun SCXW104780834 BCX0">hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when total </span><span class="NormalTextRun SCXW104780834 BCX0">reproductive isolation is </span><span class="NormalTextRun SCXW104780834 BCX0">strongest.</span><span class="NormalTextRun SCXW104780834 BCX0"> Yet, understanding how </span><span class="NormalTextRun SCXW104780834 BCX0">quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species </span><span class="NormalTextRun SCXW104780834 BCX0">remains a challenging task because </span><span class="NormalTextRun SCXW104780834 BCX0">it requires studying</span><span class="NormalTextRun SCXW104780834 BCX0"> taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper </span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">Pseudochorthippus parallelus</span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">,</span><span class="NormalTextRun SCXW104780834 BCX0"> where populations that </span><span class="NormalTextRun SCXW104780834 BCX0">show multiple reproductive barriers, including hybrid male sterility,</span><span class="NormalTextRun SCXW104780834 BCX0"> hybridise in two natural hybrid zones</span><span class="NormalTextRun SCXW104780834 BCX0">.</span><span class="NormalTextRun SCXW104780834 BCX0"> </span><span class="NormalTextRun SCXW104780834 BCX0">Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, </span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">at the beginning of the last </span><span class="NormalTextRun SCXW104780834 BCX0">glacial </span><span class="NormalTextRun SCXW104780834 BCX0">cycle in Europe</span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">.</span><span class="NormalTextRun SCXW104780834 BCX0"> </span><span class="NormalTextRun SCXW104780834 BCX0">Nuclear data shows that </span><span class="NormalTextRun SCXW104780834 BCX0">contraction</span><span class="NormalTextRun SCXW104780834 BCX0">s</span><span class="NormalTextRun SCXW104780834 BCX0"> at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find </span><span class="NormalTextRun SCXW104780834 BCX0">extensive introgression throughout the </span><span class="NormalTextRun SCXW104780834 BCX0">sampled </span><span class="NormalTextRun SCXW104780834 BCX0">species range, </span><span class="NormalTextRun SCXW104780834 BCX0">irrespective of current strength of reproductive isolation. Populations</span><span class="NormalTextRun SCXW104780834 BCX0"> exhibiting hybrid male sterility</span><span class="NormalTextRun SCXW104780834 BCX0"> in two hybrid zones show </span><span class="NormalTextRun SCXW104780834 BCX0">repeatable patterns of genomic differentiation</span><span class="NormalTextRun SCXW104780834 BCX0">,</span><span class="NormalTextRun SCXW104780834 BCX0"> consistent with shared genomic constraints </span><span class="NormalTextRun SCXW104780834 BCX0">affecting ancestral divergence or with the </span><span class="NormalTextRun SCXW104780834 BCX0">role </span><span class="NormalTextRun SCXW104780834 BCX0">of those regions </span><span class="NormalTextRun SCXW104780834 BCX0">in reproductive isolation. Together, our results suggest that </span><span class="NormalTextRun SCXW104780834 BCX0">reproductive barriers that characterise late stages of species formation</span><span class="NormalTextRun SCXW104780834 BCX0"> can evolve relatively quickly within species, particularly when associated </span><span class="NormalTextRun SCXW104780834 BCX0">with</span><span class="NormalTextRun SCXW104780834 BCX0"> strong demographic changes. </span><span class="NormalTextRun SCXW104780834 BCX0">Moreover, we show that such barriers persist in the face of</span><span class="NormalTextRun SCXW104780834 BCX0"> extensive gene flow, allowing future studies to identify </span><span class="NormalTextRun SCXW104780834 BCX0">associated </span><span class="NormalTextRun SCXW104780834 BCX0">genomic regions.</span></span><span class="EOP SCXW104780834 BCX0"> </span></p>
Dataset of "Hybrid modeling on 3D hydraulic features of a step-pool unit"
<p>In this repository you can find the data for the submission "Hybrid modeling on 3D hydraulic features of a step-pool unit" by Zhang et al. to Earth Surface Dynamics.</p> <p>The topographic models of the step-pool unit made of natural stones after FAVORization in FLOW3D for the six flow rates are kept in .stl files which were named after the flow rates (L/s). The mesh size for the step-pool feature is 2.5 mm for X, Y and Z directions. The locations, water level and flow velocity for the inlet boundary in all the numerical models are presented in the excel file. </p>
Hybrid Market- and Community-Driven Strategy for Repurposing Devices for Medical Use
<p>There is a split in today's technological development between traditional proprietary-based and open community-driven development. Open development ( open science / open software / open hardware ) often loses steam when capital and long-term commitment is required. Proprietary-based development solves the issue by attracting capital, but the need minimize and compensate risks leads to secrecy and a focus on developed economies.<br> <br> Here I propose a strategy to reconcile the two worlds. I focus on the scenario of off-the-shelf devices that can be repurposed for meeting needs in the medical field, as it can lower the typically high initial capital required in the medical device sector while motivating community involvement. The strategy is contingent on the owner of the initial technology not being deprived of its intellectual property rights.<br> <br> This is a work in progress that will be updated through my own involvement and that of any interested bodies.</p>
Data from: Reduced mitochondrial respiration in hybrid asexual lizards
<p><span>The scarcity of asexual reproduction in vertebrates alludes to an inherent cost. Several groups of asexual vertebrates exhibit lower endurance capacity (a trait predominantly sourced by mitochondrial respiration) compared to congeneric sexual species. Here we measure endurance capacity in five species of <i>Aspidoscelis </i>lizards and examine mitochondrial respiration between sexual and asexual species using mitochondrial respirometry. Our results show reduced endurance capacity, mitochondrial respiration, and phenotypic variability in asexual species compared to parental sexual species along with a positive relationship between endurance capacity and mitochondrial respiration. Results of lower endurance capacity and lower mitochondrial respiration in asexual <i>Aspidoscelis </i>are consistent with hypotheses involving mitonuclear incompatibility.</span></p> <p><span>This repository includes files with DNA sequence alignments, evolutionary relationships, mitochondrial respiration, and endurance measurements for five species of whiptail lizards. Code used to analyze the data in the context of the study is also included.</span></p>
Data files for "Hybrid quantum-classical approach for coupled-cluster Green's function theory"
<p>Source code and data files for the manuscript "Hybrid quantum-classical approach for coupled-cluster Green's function theory."</p> <p>Reference: Quantum 6, 675 (2022); https://doi.org/10.22331/q-2022-03-30-675.</p> <p>Title: Hybrid quantum-classical approach for coupled-cluster Green's function theory</p> <p>Authors: Trevor Keen, Bo Peng, Karol Kowalski, Pavel Lougovski, and Steven Johnston.</p> <p>Abstract: The three key elements of a quantum simulation are state preparation, time evolution, and measurement. While the complexity scaling of dynamics and measurements are well known, many state preparation methods are strongly system-dependent and require prior knowledge of the system’s eigenvalue spectrum. Here, we report on a quantum-classical implementation of the coupled-cluster Green’s function (CCGF) method, which replaces explicit ground state preparation with the task of applying unitary operators to a simple product state. While our approach is broadly applicable to a wide range of models, we demonstrate it here for the Anderson impurity model (AIM). The method requires a number of T gates that grow as $O(N^5)$ per time step to calculate the impurity Green’s function in the time domain, where N is the total number of energy levels in the AIM. For comparison, a classical CCGF calculation of the same order would require computational resources that grow as $O(N^6)$ per time step.</p>
Monitoring DNA hybridization with Organic Electrochemical Transistors functionalized with Polydopamine
<p>Dataset of the paper "Monitoring DNA hybridization with Organic Electrochemical Transistors functionalized with Polydopamine" published in<em> Macromolecular Materials and Engineering</em>, DOI:10.1002/mame.202100880</p> <p>The data in the excel file are organized as follows:</p> <p>In <strong>Transfer_fc-target</strong> tab is reported the mean of the I<sub>DS </sub>vs V<sub>GS</sub> curves for each of the datasets, for every concentration of fc-target.</p> <p>In <strong>Transfer_pc-target</strong> tab is reported the mean of I<sub>DS </sub>vs V<sub>GS</sub> curves for each of the datasets, for every concentration of pc-target.</p> <p>In <strong>Transfer_nc-target</strong> tab is reported the mean of the I<sub>DS </sub>vs V<sub>GS</sub> curves for 0 and 100 nM nc-target.</p> <p>In the <strong>CV</strong> tab, we show the potential vs Ag/AgCl and the current of the Cyclic Voltammetry of every gate functionalization step, shown in figure 1c of the manuscript.</p>
Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.
<p>The crustacean marine isopod species <i>Haploniscus bicuspis</i> (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using Confocal Laser Scanning Microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably characterize different male developmental stages.</p>
Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. --
Simulation files to accompany the manuscript "Two-dimensional basin-scale seismic site effects in the Kitimat Valley, British Columbia, Canada: A practical example of using a fast hybrid FE/BE method"
<p>Simulation files to accompany the two-dimensional basin-scale seismic site effects investigation in the Kitimat valley, located in the northern coastal region of British Columbia, Canada.</p>
Morphological measurements Oryzias eversi, Oryzias nigrimas and hybrids
<p><span><span><span><span><span><span><span><span><span><span><span>The evolution of complex phenotypes like reproductive strategies is challenging to understand as they often depend on multiple adaptations, which only jointly result in a specific functionality. Sulawesi ricefishes (Adrianichthyidae) evolved a reproductive strategy termed pelvic brooding. In contrast to the more common transfer brooding, female pelvic brooders carry an egg-bundle connected to their body for weeks until the fry hatches. To examine the genetic architecture of pelvic brooding, we crossed the pelvic brooding <i>Oryzias eversi</i> and the transfer brooding <i>O. nigrimas</i> (species divergence time: ~ 3.6 my). We hypothesize, that a low number of loci and modularity have facilitated the rapid evolution of pelvic brooding. Traits associated to pelvic brooding, like rib length, pelvic fin length and morphology of the genital papilla were correlated in the parental species but correlations were reduced or lost in their F1 and F2 hybrids. Using the Castle-Wright estimator, we found that generally few loci underlie the studied traits. Further, both parental species showed modularity in their body plans. In conclusion, morphological traits related to pelvic brooding were based on a few loci and the mid-body region likely could evolve independently from the remaining body parts. Both factors presumably facilitated the rapid evolution of pelvic brooding.</span></span></span></span></span></span></span></span></span></span></span></p>
Dataset from: Morphometric analyses of leaf shapes in four sympatric Medi-terranean oaks and hybrids in the Algerian Kabylie fores
<p>Data correspond to the characterization of putative hybrids and oak species coexisting in a highly diversified oak forest in Algeria with four native oak species (<em>Quercus suber</em>, <em>Q. ilex</em>, <em>Q. canariensis</em>, and <em>Q. afares</em>). Sixteen plots, including 89 trees from the four native species and their putative hybrids were sampled. Leaves were scanned and their geometric morphometry analyzed by using 11 landmarks on the right side on their abaxial surface. Related paper: Akli, A.; Lorenzo, Z.; Alia, R.; Rahbi, K.; Torres, E. Morphometric analyses of leaf shapes in four sympatric Mediterranean oaks and hybrids in the Algerian Kabylie forest. <em>Forests </em><strong>2022</strong>, <em>13</em>(4), 508 <a href="https://doi.org/10.3390/f13040508">https://doi.org/10.3390/f13040508</a></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.