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Supplementary figures and data for "Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation"

Supplementary figures and data for "Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation" by Ivan L. F. Magalhaes, Pedro H. Martins, Bárbara T. Faleiro, Teofânia H. D. A. Vidigal, Fabrício R. Santos, Leonardo S. Carvalho, Adalberto J. Santos, submitted to Cladistics.  Supplementary Figures S1 – S15 Supplementary data S16: Complete specimen data of specimens used as vouchers for morphological scorings in Excel spreadsheet format. Supplementary data S17: Discrete character matrix with morphological scorings in Nexus format. Supplementary data S18: Complete specimen data of specimens used as vouchers for DNA sequencing in Excel spreadsheet format. Supplementary data S19: Alignment of cytochrome oxidase I sequences in Fasta format. Supplementary data S20: Alignment of histone H3 sequences in Fasta format. Supplementary data S21: Alignment of 28S ribosomal sequences in Fasta format. Supplementary data S22: Alignment of internal transcribed spacer sequences in Fasta format. Supplementary data S23: Alignment of 16S ribosomal sequences in Fasta format. Supplementary data S24: Zipped folder containing the inputs for estimating the phylogeny using morphological data in IQ-Tree: matrix in nexus format, partition file, and command file in plain text. Supplementary data S25: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with Muscle in IQ-Tree: matrix in nexus format, partition file, and command file in plain text. Supplementary data S26: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with MAFFT in IQ-Tree: matrix in nexus format, partition file, and command file in plain text. Supplementary data S27: Zipped folder containing the inputs for estimating the phylogeny using morphological and sequence data aligned with MUSCLE in IQ-Tree: matrix in nexus format, partition file, and command file in plain text. Supplementary data S28: Input Nexus for estimating the phylogeny using morphological data in MrBayes. Supplementary data S29: Input Nexus for estimating the phylogeny using sequence data aligned with Muscle in MrBayes. Supplementary data S30: Input Nexus for estimating the phylogeny using sequence data aligned with MAFFT in MrBayes. Supplementary data S31: Input Nexus for estimating the phylogeny using morphological and sequence data aligned with Muscle in MrBayes. Supplementary data S32: Input XML for estimating the dated phylogeny under Bayesian inference in BEAST. Supplementary data S33: Distribution maps for all Micrathena species included in this study, the database with the original records and their source, and the R script used to generate the maps. Supplementary data S34: Zipped folder containing all the inputs for estimating ancestral ranges and performing biogeographic stochastic mapping in R. This contains (0) the scripts for performing model selection and estimating ancestral states over a distribution of posterior trees, followed by stochastic mapping; (1) the geography and tree files (MMCT, and 100 trees randomly drawn from the posterior distribution);  (2) the dispersal matrix and (3) the files for performing the time-stratified analysis to test the influence of the closure of the Isthmus of Panama on Micrathena dispersal. Supplementary data S35: R script for generating the in-situ-speciation-through-time graphs from the results of biogeographic stochastic maps, as seen in Fig. 5. Supplementary data S36: R script for getting and plotting elevations from individual records of Micrathena. Supplementary data S37: R script for performing the GeoHiSSE estimation of net diversification rates among areas. Supplementary data S38: Zipped folder containing the optimal trees found as a result of analysing inputs S24–S32 (IQ-Tree, MrBayes and BEAST). Supplementary data S39: Zipped folder containing the ancestral range estimation results under competing models in BioGeoBEARS. Supplementary data S40: Excel spreadsheet with parameter values of competing biogeographic models in BioGeoBEARS. Supplementary data S41: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes all Micrathena species. Supplementary data S42: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes only Micrathena species which had their DNA sequenced. Supplementary data S43: Excel spreadsheet with the geography matrix, indicating which Micrathena species may be found in each area, and indicating the proportion of species from each area that are missing from the incomplete dataset  (i.e., excluding species with unavailable DNA sequences). Supplementary data S44: Excel spreadsheet with parameter values of competing biogeographic models estimated in GeoHiSSE.

Supplementary data: Exploring Remanufacturing Conveniency: An Economic and Energetic Assessment for a Closed-Loop Supply Chain of a Mechanical Component

The conveniency between remanufacturing a single mechanical product and its new production is a highly investigated topic across various disciplines, including supply chain management. To this end, a comparison was made among three different configurations of the supply chain network: the traditional network for new production, the network with remanufacturing and direct interaction between customer and manufacturer, and the network with remanufacturing and indirect interaction between customer and manufacturer through a distribution center. The evaluation of scenarios for the remanufacturing conveniency of remanufacturing was conducted from both an economic and energetic perspective, generating 10'000 cases using the Sobol quasi-random low-discrepancy sequence. The generation was carried out for both economic and energetic analyses for three types of materials, namely steel, aluminum, and titanium, for which complete datasets are provided: <ul> <li>Steel_EconomicAnalysis.xlsx: dataset for economic analysis for the remanufacturing conveniency of mechanical products in steel</li> <li>Steel_EnergeticAnalysis.xlsx: dataset for energetic analysis for the remanufacturing conveniency of mechanical products in steel</li> <li>Aluminum_EconomicAnalysis.xlsx: dataset for economic analysis for the remanufacturing conveniency of mechanical products in aluminum</li> <li>Aluminum_EnergeticAnalysis.xlsx: dataset for energetic analysis for the remanufacturing conveniency of mechanical products in aluminum</li> <li>Titanium_EconomicAnalysis.xlsx: dataset for economic analysis for the remanufacturing conveniency of mechanical products in titanium</li> <li>Titanium_EnergeticAnalysis.xlsx: dataset for energetic analysis for the remanufacturing conveniency of mechanical products in titanium</li> </ul>

opencc-by-4.0Jan 2024View details →

Supplementary Data for "Exploring the Chemical Space of Metal–Organic Frameworks with rht Topology for High Capacity Hydrogen Storage"

This dataset includes optimization and simulation inputs, optimized structures, building blocks, computed hydrogen uptakes and textural properties of the metal–organic frameworks that correspond with work in "Exploring the Chemical Space of Metal–Organic Frameworks with rht Topology for High Capacity Hydrogen Storage" (DOI: 10.1021/acs.jpcc.4c00638).

Supplementary File 8; The full data set derived from formal quantitative surveys of land cover types and activities of humans, livestock and wildlife (Section 2.3) that were used for the analyses described in sections 2.4, 2.5 and 2.7

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opencc-zeroMay 2024View details →

Supplementary data for: Outmigrating central valley Chinook Salmon

Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of Central Valley Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of Central Valley Chinook salmon that allows inclusion of relatively low-quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late-fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in Central Valley Chinook salmon, and demonstrates the power of genomics-based population assignments to aid the study and management of intraspecific diversity.

Costless correction of chain based nested sampling parameter estimaion in gravitational wave data and beyond (supplementary material)

These are the nested sampling inference products used to obtain the results for <a href="https://arxiv.org/abs/2404.16428">arXiv:2404.16428</a>. The chains are given as pickled dataframes as there are over 1000 runs provided here. The script for reproducing the plots in the paper is also given.  Folders: outdir_simulated_BBH - contains 200 runs on the same simulated signal. 'samples' contains the full sets of weighted samples from each run and 'full_dfs' contains the dataframes with the weighted samples AND the phantom points from the run. The samples in 'full_dfs' with chain_no=0 are the weighted samples, and all others are phantoms.  outdir_test - contains the single run on the above simulated signal which was performed with num_repeats=25*ndims=100.  outdir_coverage - contains 1000 runs on different simulated signals, with parameters drawn from the prior. The drawn values are saved as '{}_params.npy' for each run.

Supplementary Data for 'Eastern Australian estuaries will transition to tidal flood regimes in coming decades' by Hague, Thran, Jakob and Jones.

Supplementary data to support Hague et al. (2024) Coastal Futures paper, Eastern Australian estuaries will transition to tidal flood regimes in coming decades. column 'UTC_DT' provides datetime information in UTC in format YYYY-MM-DD hh:mm:ss column 'sea_lvl' provides quality assured water level as described in Hague et al. (2024) column 'sea_lvl'_pred' provides estimate of tidal contribution to water level as described in Hague et al. (2024)

opencc-zeroMay 2024View details →

Supplementary code and data for: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee

<div> <div> <div> Host-microbe interactions underlie the development and fitness of many macroorganisms, including bees. Whereas many social bees benefit from vertically transmitted gut bacteria, current data suggests that solitary bees, which comprise the vast majority of species diversity within bees, lack a specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of the ground-nesting solitary bee Anthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacterial genera (Streptomyces, Nocardiodes) and the fungus Moniliella spathulata. Dormant (diapausing) larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for diapausing bees. First, using isolated bacteria and fungi, we found that Streptomyces from brood cells inhibited the growth of multiple pathogenic filamentous fungi, suggesting a role in pathogen protection during overwintering, when bees face high pathogen pressure. Second, sugar alcohol composition changed in tandem with major changes in fungal abundance, suggesting links with bee cold tolerance or overwintering biology. We find that Anthophora bomboides hosts a conserved core microbiome that may provide key fitness advantages through larval development and diapause, which raises the question of how this microbiome is maintained and faithfully transmitted between generations. Our results suggest that focus on microbiomes of mature or active insect developmental stages may overlook stage-specific symbionts and microbial fitness contributions during host dormancy. </div> </div> </div>

Supplementary data to "High-Resolution Raman Imaging of >300 Patient-Derived Cells from Nine Different Leukemia Subtypes: A Global Clustering Approach"

Compressed ".feather" files including the entire dataset of 319 Raman maps of the same number of cells from 19 patients affected by nine distinct leukemia subtypes. Raw data have been pre-processed as follows using custom software (LabVIEW, National Instruments Corp., TX):  a) cosmic rays removal by singular value decomposition (SVD); b) camera offset subtraction; c) CCD response correction (intensity and etaloning) using a tungsten halogen light with known emission (Avalight-HAL, Avantes BV, NL)); d) wavenumber calibration using the zero-wavenumber laser line, toluene and argon-mercury emission (CAL-2000, Ocean Optics, Germany); e) denoising by SVD. More details in the open access published article and supplementary material (10.1021/acs.analchem.4c00787).

Supplementary data to "Quantum-critical properties of the one- and two-dimensional random transverse-field Ising model from large-scale quantum Monte Carlo simulations"

This dataset contains the data used to generate the results in the work "Quantum-critical properties of the one- and two-dimensional random transverse-field Ising model from large-scale quantum Monte Carlo simulations" [1]. processed_data.zip contains the data used for the figures shown in [1], while raw_data.zip contains the original simulation results without further processing. To get an overview of the organization of the directories and a description of the data we recommend the README files in the top- and subdirectories. [1] C. Krämer et al., Quantum-critical properties of the one- and two-dimensional random transverse-field Ising model from large-scale quantum Monte Carlo simulations, <a href="https://doi.org/10.48550/arXiv.2403.05223">10.48550/arXiv.2403.05223</a>, 2024

Data, code and supplementary material - Gone but not forgotten: dynamics of sperm storage and potential ejaculate digestion in the black soldier fly Hermetia illucens

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Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes"

Supplementary Data for "Phylogeny and evolution of dissimilatory sulfite reduction in Prokaryotes" Supplementary Data 1: The information of the genomes we used in our analyses. The “DsrAB” sheet included the information of DsrAB-containing genomes and denoted whether DsrC, DsrM, DsrK, DsrJ, DsrO, DsrP genes were present. The other sheets included the information of the representative genus-level genomes which comprised DsrAB. These genomes were used to reconstruct genus-level phylogenies to compare tree topologies within phylum. See the “Note” sheet for more details. Supplementary Data 2: The raw data of Ka/Ks values of each gene pair estimated by KaKs_calculator v2.0 with MA method. Supplementary Data 3: the information of the COGs of iron-reducers and SRMs, respectively. Supplementary Data 4: fasta files used for tree reconstruction, including Dsr-related proteins and concatenated sequences for phylogenomic trees. The folder names indicated their analytical purposes. Supplementary Data 5: tree files used in our analyses, including Dsr trees, genetic distance-based trees and dated phylogenetic trees. The folder names indicated their analytical purposes.

opencc-zeroJun 2024View details →

Data and supplementary information from: Sequential bayesian phylogenetic inference

The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from a given analysis is used as input for the next analysis (e.g., a single multiple sequence alignment is used to estimate a gene tree). In this framework, uncertainty is not propagated from step to step, which can lead to inaccurate or spuriously certain results. Here, we formally develop and test the sequential approach for Bayesian phylogenetic inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior produced in the previous step. The sequential approach presented here not only accounts for uncertainty between analysis steps, but also allows for greater flexibility in software choice (and hence model availability) and can be more efficient computationally than the traditional joint approach when multiple models are being tested. We show that the sequential approach is identical in practice to the joint approach only if sufficient information in the data is present (a narrow posterior distribution) and/or sufficiently many importance samples are used. Conversely, we show that the common practice of using a single point estimate can be biased, e.g., a single phylogeny estimate to transform an unrooted phylogeny into time-calibrate phylogeny. We demonstrate the theory of sequential Bayesian inference using both a toy example and an empirical case study of insect divergence times estimation using a relaxed clock model from transcriptome data. In the empirical example, we estimate three posterior distributions of branch lengths from the same data (DNA character matrix with a GTR+Gamma+I substitution model, an amino acid data matrix with empirical substitution models, and an amino acid data matrix with the PhyloBayes CAT-GTR model). Finally, we apply three different-node calibration strategies and show that both, the data source and underlying substitution process to estimate branch lengths as well as the node-calibration strategies, impact divergence time estimates. Thus, our new sequential Bayesian phylogenetic inference provides the opportunity to efficiently test different approach for divergence time estimation, including branch lengths estimation from other software.

Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen - Supplementary Data files

Supplementary Data file 3-4 included in the manuscript Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen.

Supplementary data for "Seasonal emergence and circulation coupling of moist layers over the tropical Atlantic"

The data provided here contains the derived moist layer characteristics from ERA5 reanalysis, as presented in the associated publication. Data is given on a 0.25° latitude/longitude grid between 30°N/S on the native vertical levels of the ERA5 dataset, cut off at 50 hPa. When a moist layer is detected at a given location and altitude, as identified by the method described in Sect. 2.2 of the publication, the moist layer characteristics (strength, pressure level, upper bound pressure, lower bound pressure) are written in the associated files at the given location (lat/lon) and pressure level of the moist layer. Here, we provide the 15 year means and standard deviations for the months January and July, and the 3 hourly data along the equatorial and 15°N cross-sections of the Atlantic used for the Hovmoller diagrams in Fig. 4 and Supporting Figure S1 of the publication. Files containing "geographical_mean" indicate monthly means on the latitude/longitude grid. Files containing "moisture_space" indicate monthly means within moisture space over the tropical Atlantic, as defined in the paper.  Code used to generate the data and to conduct the analysis presented in the publication are provided in the github repository URL listed in the Software section.

Supplementary File 10; The full data set used for the analysis presented herein:

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Supplementary data for the paper: "Self-healing concrete with a bacteria-based or crystalline admixture as healing agent to prevent chloride ingress and corrosion in a marine environment'"

<div> Supplementary data for the paper:  "Self-healing concrete with a bacteria-based or crystalline admixture as healing agent to prevent chloride ingress and corrosion in a marine environment" Open data concerning experimental work. Bacteria-based agents (BAS) and crystalline admixtures (CA) are explored as healing agents to enhance chloride resistance and prevent corrosion. Healing of 100 µm and 300 µm wide cracks was investigated, in combination with two conditioning methods. Either the samples were subjected to wet/dry cycles for 3 months before exposure (“healed”), or they were directly exposed to artificial seawater after crack creation (“unhealed”).  </div> <h2>Files</h2>

opencc-zeroJun 2024View details →

Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

Based on past and expanded DNA sampling, the orthopteran families Stenopelmatidae and Anostostomatidae, as currently structured, are shown to be non-monophyletic. The splay-footed cricket genus Comicus, is confirmed to be genetically distinct from all Stenopelmatidae. We add two specimens to our previously published phylogenetic tree for New World Stenopelmatus Jerusalem cricket species and report the first multilocus DNA recovery for S. ater from Costa Rica. Male internal genitalia may be of systematic value in Jerusalem crickets, but we believe they should be analyzed when in their unfolded, "physiologically functional" state, where morphological characters can be seen in more detail when compared to their preserved, folded state. We describe Stenopelmatus nuevoguatemalae n. sp. from Guatemala.

opencc-by-4.0Feb 2024View details →

Supplementary Data: Human settlement pressure drives slow-moving landslide exposure

These datasets (.Rmd, .Rroj., .rds) are ready to use within the R software for statistical programming with the R Studio Graphical User Interface (https://posit.co/download/rstudio-desktop/). Please copy the folder structure into one single directory and follow the instructions given in the .Rmd file. Files and folders are described in the README.md file 0_ferrer_etal_2024.Rproj README.md 1_R_Notebook: <ul> <li>SlowMovingLandslide_Exposure.rmd</li> <li>Ferrer2024_FloodExposureAnalysis.Rmd</li> </ul> 2_data: <ul> <li>1_input: <ul> <li>sm_database_2023_01_17.csv</li> <li>sm_database_references.pdf</li> <li>gmba_v2</li> <li>ipcc_regions</li> <li>natrual_earth</li> </ul> </li> <li>2_processed: <ul> <li>model_data_2023_01_17.csv</li> <li>summary_database.csv</li> </ul> </li> </ul> 3_results: <ul> <li>1_model <ul> <li>2023_12_31.model.rds</li> </ul> </li> <li>2_figures: <ul> <li>main_figure_elements</li> </ul> </li> <li>3_ext_figures</li> </ul> 4_manuscript_figures: <ul> <li>1_main figures</li> <li>2_extended_figures</li> </ul> 5_floding_analysis: <ul> <li>flood_comp_mod.csv</li> <li>flood_comp_model.rds</li> </ul>