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Data accompanying the manuscript "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies"
<p>Dataset for figures 2, A6 and A8 for the manuscript: "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies." The dataset contains the optimal protocols for Majorana transport in both the Kitaev Chain model as well as the Proximity Coupled Semiconduncting Nanowire model obtained with Differentiable Programming and Natural Evolution Strategies. Also the Simulated Annealing (SA) optimal protocols for the Kitaev chain are included.</p>
Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis
<p>Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. While convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in <i>Myotis</i> bats, the only Chiropteran genus with a worldwide distribution. Three foraging strategies –gleaning, trawling, and aerial netting– repeatedly evolved in several regions of the world, each linked to characteristic morphologies recognized as ecomorphs. Phylogenomic, morphometric, and comparative approaches were adopted to investigate convergence of such foraging strategies and skull morphology as well as factors that explain diversification rates. Genomic and morphometric data were analyzed from ~80% extant taxa. Results confirm that the ecomorphs evolved multiple times, with trawling evolving more often and foliage gleaning most recently. Skull morphology does not reflect common ancestry, evolves convergently with foraging strategy. While diversification rates have been roughly constant across the genus, speciation rates are area-dependent in taxa with temperate distributions. Results suggest that in this species-rich group of bats, first, stochastic processes have led divergence into multiple lineages. Then, natural selection in similar niches has promoted repeated adaptation of phenotypes and foraging strategies. <i>Myotis</i> bats are thus a remarkable case of ecomorphological convergence and an emerging model system for investigating the genomic basis of parallel adaptive radiation.</p>
COCO BBOB-constrained Benchmark Results of Two Evolution Strategy Variants
<p>The three zip-files of this data set provide the performance data of the algorithms presented in the paper<strong> "Benchmarking 𝜖MAg-ES and BP-𝜖MAg-ES on the bbob-constrained Testbed"</strong> submitted to the GECCO 2022 Workshop "<a href="https://gecco-2022.sigevo.org/Workshops#BBOB 2022">BBOB 2022 — Black Box Optimization Benchmarking 2022</a>".</p> <ul> <li><em>coco2.6.2_bbob-constrained_epsMAg.zip</em> <-- results of the 𝜖MAg-ES on COCO version 2.6.2</li> <li><em>coco2.6.2_bbob-constrained_BPepsMAg.zip</em> <-- results of the BP-𝜖MAg-ES on COCO version 2.6.2</li> <li><em>coco2.6.2_bbob-constrained_fmincon</em><em>.zip</em> <-- results of FMINCON (Matlab 2021b) on COCO version 2.6.2</li> </ul> <p> </p>
Fig. 2 in The oldest isorophid edrioasteroid (Echinodermata) and the evolution of attachment strategies in Cambrian edrioasteroids
Fig. 2. Edrioasteroid Protorophus hispanicus gen. et sp. nov., Purujosa (Zaragoza Province, Spain). Holotype MPZ2009/1233 in adoral (A) and aboral (B) views; camera lucida drawing of the adoral view (C) with interpretation of major anatomical structures; camera lucida drawing of the aboral face (D). Note the base of the flooring plates. Scale bar is 1 mm for all specimens. Photographs are taken from latex casts whitened with NH4Cl sublimate. Abbreviations: LAO, left anterior oral plate; LBO, left branching oral plate; RAO, right anterior oral plate; RBO, right branching oral plate.
Fig. 4 in The oldest isorophid edrioasteroid (Echinodermata) and the evolution of attachment strategies in Cambrian edrioasteroids
Fig. 4. New edrioasteroid from the middle Cambrian of China (Zhao et al. in press). A. Adoral view of an adult specimen GM2103. B. Adoral view of a juvenile specimen GM1331 C. Aboral view of a juvenile specimen GM1670. B, C show a marginal ring. Photographs are taken from latex casts whitened with NH4Cl sublimate. Courtesy of Colin Sumrall.
Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g are referred to in the text.
Figure 10 in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 10. The EES axes and values of morphometric variation that support a revised soldier defence classification. a, Planicapritermes; b, Dihoplotermes; c, Cavitermes; d, Termes.
Figure 4 in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 4. Outline data treatment for eigenshape analysis. Original outline described by 300 x,y points: S, start point; F, finish point; LM, landmark point. Converted to 250 equally spaced x,y coordinate points of the open outline. x,y plot of the f points with a 99% tolerance criterion to retain the outline between LM, S and F points.
Figure 2. x,y in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 2. x,y coordinate outline data are converted to a series of f (angular deviation) data points, which have been plotted. The position of the geometric landmark for extended eigenshape analysis is labelled.
Figure 1 in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 1. The soldier termite mechanical defensive mechanisms described by Prestwich (1984). Reprinted with permission, from the Annual Review of Entomology, Volume 29 © 1984 by Annual Reviews http://www.annualreviews.org
Figure 5. Head capsule EES plots. A, axis 2 in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 5. Head capsule EES plots. A, axis 2 vs. axis 1. B, axis 2 vs. axis 3. C, modelled mode of dorsal head capsule shape change along axes 1, 2 and 3.
Figure 3 in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology
Figure 3. Soldier head features independently analysed; straight lines represent the size measurements: dots, landmark points; S, start point; F, finish point.
Replication data in the form of simulation outputs for "The joint evolution of animal movement and competition strategies"
<p>This version of the data is a re-upload of an identical dataset uploaded to DataverseNL. The data are being uploaded here for uniformity of archiving with the other supplementary materials accompanying the manuscript, "The joint evolution of animal movement and competition strategies", which is accepted for publication in <em>The American Naturalist</em>.</p> <p>The dataset consists of a single zipped folder, data/, which contains subfolders with the simulation specific data. These subfolders are named 'sim_SCENARIO_rep_NNN_gro_RMAX', where 'SCENARIO' refers to the three scenarios of the model described in our manuscript, 'NNN' is the replicate number, and 'RMAX' is the maximum cell productivity in that simulation.</p> <p>Each of the subfolders consists of the following:</p> <ol> <li>The directory ‘depends/’, which holds the ‘extract.exe’ program. This program is used to extract specific data from the stored simulation output.</li> <li>The ‘sourceMe.R’ file allows the ‘extract.exe’ program to be linked to R, delivering the required data as a list object that can be handled in R.</li> <li>The stored simulation data on agents, as a series of ‘.arc’ and ‘.bin’ files.</li> <li>The ecological snapshots of the landscape, with prey items, foragers, kleptoparasites, and handlers (depending on the scenario), which are stored as PNG files named ‘00NNN.png’, where NNN is a three digit representation of the generation number (e.g. 001 for generation 1).</li> <li>Cumulative sums of the numbers of prey items, foragers, kleptoparasites, the intake from foraging (searching for prey), and the intake from the kleptoparasitic strategy (searching for handlers), on each cell of the landscape, for each of the last 9 generations of the simulation, as ‘NNN.txt’, where LAYER may be ‘items’ (prey items), ‘foragers’ (foragers), ‘klepts’ (kleptoparasites), ‘foragers_intake’ (the intake from the foraging strategy), or ‘klepts_intake’ (the intake due the kleptoparasite strategy. NB: These files are not used in our analyses, and may be ignored.</li> </ol> <p>'SCENARIO' may be one of “foragers” (scenario 1), “obligate” (scenario 2), or “facultative” (scenario 3).</p> <p>'NNN' may be one of “001”, “002”, or “003”.</p> <p>'RMAX' may be one of “0.001”, “0.005”, “0.01”, “0.02”, “0.03”, “0.04”, or “0.05”. The manuscript presents results for 'RMAX' = 0.01.</p>
Reference data from the Pathomove simulation, for the manuscript "Novel pathogen introduction triggers rapid evolution in animal social movement strategies"
<p>This is a reference dataset of multiple runs of the 'Pathomove' simulation, to accompany the manuscript "Novel pathogen introduction rapidly alters the evolution of movement, restructuring animal societies". The datasets are in the form of R data objects saved as Rds files.</p> <p>This version of the data is intended to accompany a resubmission to <em>eLife</em>.</p>
Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis
Open the record for dataset details and reuse information.
The importance of evolutionary timelines when explaining the evolution of parental care strategies
Open the record for dataset details and reuse information.
An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans
<p>Dizygotic twinning, the simultaneous birth of siblings when multiple ova are released, is an evolutionary paradox. Twin bearing mothers often have elevated fitness<sup>1-5</sup>; but despite twinning being heritable<sup>6</sup>, twin births only occur at low frequencies in human populations<sup>7</sup>. We resolve this paradox by showing that twinning and non-twinning are not competing strategies, instead dizygotic twinning is the outcome of an adaptive conditional ovulatory strategy of switching from single to double ovulation with increasing age. This conditional strategy when coupled with the well-known decline in fertility as women age, maximizes reproductive success and explains the increase and subsequent decrease in twinning rate with maternal age that is observed across human populations<sup>8-10</sup>.<span> We show that the most successful ovulatory strategy would be to always double ovulate as an insurance against early fetal loss, but to never bear twins. This finding supports the hypothesis that twinning is a byproduct of selection for double ovulation rather than twinning.</span></p>
Dataset of ""Statistical atlases and automatic labelling strategies to accelerate the analysis of social insect brain evolution"
<p>Dataset of <em>Statistical atlases and automatic labelling strategies to accelerate the analysis of social insect brain evolution</em> by Sara Arganda, Ignacio Arganda-Carreras, Darcy G. Gordon, Andrew P. Hoadley, Alfonso Pérez-Escudero, Martin Giurfa and James F. A. Traniello.</p> <p>In this dataset, we are presenting:</p> <ul> <li>10 confocal brain images from <em>Pheidole spadonia </em>minors (in the original confocal TIFF format and in the open NRRD format), with manually segmented labels of 8 subregions (Optic Lobes, OL; Antennal Lobes, AL; Mushroom Body Medial Calyx, MB-MC; Mushroom Body Lateral Calyx, MB-LC; Mushroom Body Peduncle, MB-P; Central Complex, CX; Subesophageal zone, SEZ; and Rest of Central Brain, ROCB – in NRRD format) from one expert annotator.</li> <li>12 confocal brain images from <em>P. spadonia</em>, <em>P. rhea</em>, <em>P. tepicana</em> and <em>P. obtusospinosa</em> minors, with manually segmented labels of the same 8 subregions (OL; AL; MB-MC; MB-LC; MB-P; CX; SEZ; and ROCB) from one expert annotator.</li> <li>5 confocal brain images from <em>Pheidole spadonia </em>minors (“test brains”), with five sets of manually segmented labels of the same 8 subregions (OL; AL; MB-MC; MB-LC; MB-P; CX; SEZ; and ROCB) from three expert annotators (one set from annotator 1, one set from annotator 2 and three sets from annotator 3, to evaluate inter and intra person differences).</li> <li>1 group-wise template generated from the 10 confocal brain images from <em>Pheidole spadonia </em>minors, with three sets of manually segmented labels of the same 8 subregions (OL; AL; MB-MC; MB-LC; MB-P; CX; SEZ; and ROCB).</li> <li>5 group-wise templates generated from the 9 confocal brain images from <em>Pheidole spadonia </em>minors, with consensus labels of the same 8 subregions (OL; AL; MB-MC; MB-LC; MB-P; CX; SEZ; and ROCB).</li> <li>1 group-wise template generated from 12 confocal brain images from <em>P. spadonia</em>, <em>P. rhea</em>, <em>P. tepicana</em> and <em>P. obtusospinosa</em> minors, with consensus labels of the same 8 subregions (OL; AL; MB-MC; MB-LC; MB-P; CX; SEZ; and ROCB).</li> <li>7 sets of automatic labels for the 5 “test brains”: 3 sets of “Direct Labels”, 3 sets of “Consensus Labels”, 1 set of “Multispecies Template Labels”.</li> </ul> <p>Brain of minor workers were dissected from the ant head capsule in ice cold HEPES-buffered saline and were fixed and immunohistochemically stained using SYNORF1 (a monoclonal <em>Drosophila</em> synapsin I antibody obtained from the Developmental Studies Hybridoma Bank, catalog 3C11) and secondarily stained using Alexa Fluor 488 for visualization of neuropil (slightly modified from Ott, 2008). Later, brains were mounted in methyl salicylate and imaged on an Olympus Fluoview BX50 laser scanning confocal microscope with a ×20 objective at a resolution of ~0.7 × 0.7 × 5µm/voxel. All brain tissue manipulation, staining and recording was performed by Darcy G. Gordon. Brain images were obtained in TIFF format by the confocal microscope and then opened and saved as Amira Mesh (.am) stack images in Amira (version 6.0). Manual segmentation of each brain was done using Amira (version 6.0 or 2019.2). Labels were traced on eight compartments in only one brain hemisphere, except for the CX, SEZ and ROCB, which lack a clear subdivision between hemispheres. Brain grey image stacks and labels were transformed to NRRD format for template construction using the Fiji plugin SaveAsGzipNrrd<a href="#_ftn1">[1]</a>. Volume and volume similarity of labels were calculated using the Fiji toolbox MorphoLibJ<a href="#_ftn2">[2]</a>.</p> <p><strong>Acknowledgements: </strong>We thank Ming Huang (from Dr. Diana Wheeler’s laboratory) who kindly provided access to colonies from four species of the hyperdiverse ant genus <em>Pheidole</em> (<em>P. spadonia</em>, <em>P. rhea</em>, <em>P. tepicana </em>and <em>P. obtusospinosa</em>). This research was supported by National Science Foundation grants IOS 1354291 and IOS 1953393 to JT, a Marie Skłodowska-Curie Individual Fellowship BrainiAnts-660976 and Ayudas destinadas a la atracción de talento investigador a la Comunidad de Madrid en centros de I+D. This work is supported in part by the University of the <a href="https://www.sciencedirect.com/topics/engineering/basque-country">Basque Country</a> UPV/EHU grant GIU19/027.</p> <p> </p> <p><a href="#_ftnref1">[1]</a> https://github.com/iarganda/tefor</p> <p><a href="#_ftnref2">[2]</a> https://imagej.net/plugins/morpholibj</p>
Comparative genomics reveals evolution traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae
<p><em>Botryosphaeriaceae</em>, as a major family of the largest class of kingdom fungi <em>Dothideomycetes</em>, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and bio-material plants. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted the first large-scale whole-genome comparison of 271 <em>Dothideomycetes</em>, including 19 species in <em>Botryosphaeriaceae</em>. The comparative genome analysis provided a clear classification of <em>Botryosphaeriaceae</em> in <em>Dothideomycetes</em> and indicated that <em>Botryosphaeriaceae</em> pathogenicity evolution undergoes multiple times. Mating strategies analysis demonstrated at least 3 transitions were found within <em>Botryosphaeriaceae</em> from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different species within <em>Botryosphaeriaceae</em> varied greatly, indicating that a secondary lineage expansion occurs in speciation. These findings cast new insights into evolution traits, mating strategies and pathogenicity-related genes variation of <em>Botryosphaeriaceae</em>.</p>
Evolution of a novel female reproductive strategy in Drosophila melanogaster populations subjected to long term protein restriction
<p>Reproductive output is often constrained by availability of macronutrients, especially protein. Long term protein restriction, therefore, is expected to select for traits maximizing reproduction even under nutritional challenge. We subjected four replicate populations of <em>Drosophila melanogaster</em> to a complete deprivation of yeast supplement, thereby mimicking a protein restricted ecology. Following 24 generations, compared to their matched controls, females from experimental populations showed increased reproductive output early in life, both in presence and absence of yeast supplement. The observed increase in reproductive output was without associated alterations in egg size, development time, pre-adult survivorship, body mass at eclosion, and lifespan of the females. Further, selection was ineffective on lifelong cumulative fecundity. However, females from experiment regime were found to have a significantly faster rate of reproductive senescence following the attainment of the reproductive peak early in life. Therefore, adaptation to yeast deprivation ecology in our study involved a novel reproductive strategy whereby females attained higher reproductive output early in life followed by faster reproductive aging. To the best of our knowledge, this is one of the cleanest demonstration of optimization of fitness by fine tuning of reproductive schedule during adaptation to a prolonged nutritional deprivation.</p>
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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.