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opencc-by-4.0Mar 2023View details →

Model outputs for the article "Modelling the evolution of Arctic multiyear sea ice over 2000–2018"

icemod_monthly.tar.gz contains the gridded monthly averaged quantities used in the manuscript "Modelling the evolution of Arctic multiyear sea ice over 2000-2018" for each year between 2000 and 2018. Multiyear ice variables are conc_myi (concentration of multiyear ice in a grid cell) and thick_myi (cell average thickness of multiyear ice in a grid cell, in metres), along with source and sink terms (units per day) for multiyear concentration (dci_mlt_myi, dci_ridge_myi and dci_rplnt_myi, for melt, ridging and replenishment) and volume (dvi_mlt_myi and dvi_rplnt_myi, for melt and replenishment). transports_monthly_sections.zip contains the transports of multiyear ice through the sections defining each region in Figure 8 of the paper. MYIsiaXport indicates multiyear ice area transport, while myiXport indicates multiyear ice volume transport. In case information is missing, do not hesitate to contact heather.regan@nersc.no, guillaume.boutin@nersc.no, or einar.olason@nersc.no.

opencc-by-4.0Apr 2023View details →

Morphological cladogenesis and terminal dwarfing in extinct Late Miocene through Pliocene menardiform globorotalids: New complementary data to «Evolutionary prospection in the Neogene planktic foraminifer Globorotalia menardii and related forms from ODP Hole 925B (Céara Rise, western tropical Atlantic): evidence for gradual evolution superimposed by long distance dispersal ?, Swiss J. Palaeontology, 135:205-248»

A complementary morphometric data set is provided to the study of Knappertsbusch (2016) about the shell evolution of menardiform globorotalids (Neogene planktic foraminifera) at ODP Hole 925B from Céara Rise in the the western tropical Atlantic. The new measurements confirm splitting of extinct Globorotalia multicamerata from the G. menardii stock via the intermediate form G. limbata between about 6 Ma to 5 Ma ago. After splitting both G. limbata and G. multicamerata show gradual divergence from G. menardii in several shell parameters illustrating morphological cladogenesis. Between 2.88 Ma and 2.59 Ma the same parameters show a concerted trend towards reduced values indicating pre-extinction dwarfing. A comparison with published literature data of Delta18O trends between species, that populated the mixed layer (Globigerinoides sacculifer) and the thermocline layer (Neogloboquadrina dutertrei) at this location during those times suggests, that both divergence and subsequent dwarfing trends were probably the results of changes in upper watermass stratification. The complementary data set is provided in six zipped archives APPENDIX A, B, C, D, E and F (zipped with free software 7-Zip 22.00 (x64), 2022-06-15 from 1999-2022 Igor Pawlow), together with a description of the data in file Report_925B_suppl_1.pdf.

opencc-by-4.0May 2023View details →

Evolution of model and geological inconsistencies during inversion

Supplementary material to:  Giraud, J., Caumon, G., Grose, L., Ogarko, V., and Cupillard, P.: Integration of automatic implicit geological modelling in deterministic geophysical inversion, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-129, 2023 The GIF shows a 3D view of the inverted model and its geological inconsistencies during inversion when geological correction is applied at each iteration.

opencc-by-4.0Dec 2022View details →

Data associated with the article "Evolution and phylogenetic distribution of endo-α-mannosidase"

Data associated with the article "Evolution and phylogenetic distribution of endo-α-mannosidase" Changelog: version 1.1 <ul> <li>added Tunicaraptor motif analysis alignment</li> </ul> version 1.0 <ul> <li>Initial release</li> </ul>   Funding statement: National Science Centre of Poland is acknowledged for funding of the project 2020/36/C/NZ8/00081, "The role of glycosylation in the emergence of animal multicellularity", which enabled the creation of this research output.

opencc-by-4.0Jun 2023View details →

Diversity and evolution of cerebellar folding in mammals

Coronal cerebellar mid-sections for 56 mammalian species, at the same scale.   This figure is from our open access paper: Heuer, K., Traut, N., de Sousa, A. A., Valk, S., & Toro, R. (2022). Diversity and evolution of cerebellar folding in mammals. bioRxiv. <a href="https://doi.org/10.1101/2022.12.30.522292">https://doi.org/10.1101/2022.12.30.522292</a>   Abstract The process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. We observed 2 groups of phenotypes changing concertedly through evolution: a group of “diverse” phenotypes – varying over several orders of magnitude together with body size, and a group of “stable” phenotypes varying over less than 1 order of magnitude across species. Our analyses confirmed the strong correlation between cerebral and cerebellar volumes across species, and showed in addition that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial anatomy and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. We discuss how these findings could provide new insights into the diversity and evolution of cerebellar folding, the mechanisms of cerebellar and cerebral folding, and their potential influence on the organisation of the brain across species.

opencc-by-4.0Jun 2023View details →

A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems

Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.

opencc-by-4.0Dec 2022View details →

DNA loss model explains the evolution of the neuropeptide LWamide, APGWamide, APGW/AKH, RPCH, AKH, ACP, CRZ, and GnRH families

R1: Establishment and purification of neuropeptide sequences The LW, APGW, RPCH, AKH, CRZ, and GnRH neuropeptide families were searched in the GenBank database using 10 keywords: the neuropeptide name, the precursor abbreviation, the full name of the precursor, the full name of the precursor with the word “prepropeptide,” and the combinations of these terms. The candidate sequences were downloaded in FASTA format using the appropriate commands in the GenBank database. The AKH neuropeptide family was classified according to the groups published in the literature, as well as the amino acid number and sequence. Furthermore, the ACP hybrid family was identified in the GenBank database using BLAST alignments. C00: Neuropeptide Precursor. Eight folders were named with the initials of each neuropeptide family. The AKH family folder was the only one containing four subfolders. All of the folders contained the same type of files: three text files named after the neuropeptide initials and the obtained result. The files identified with the words “with codes” contained the sequences with the codes generated for this study, whereas the documents with the word “Full” contained the GenBank database search results obtained with the 10 aforementioned keywords. These files were located in a folder named “Fasta Keywords.” Each file contained the results from each respective keyword. The files with the words “selected EA” contained the sequences that were selected for evolutionary analyses. C01: BLAST ACP. The text file named “00 BLAST ACP” contains the BLAST alignment results obtained from the NCBI database generated with the Adipokinetic Hormone/Corazonin-related peptide from the transcriptome of Callinectes toxotes. The file named “01 ACP Selected” contains the precursors selected for this study. All sequences were in FASTA format and contained the codes summarized in Supplementary Material 3 “Database Sequences.” The file named “02 ACP selected EA” contains the ACP precursors of other species, which were used for the evolutionary analyses of C. toxotes ACP. The PDF file titled “03 ACP ProP 1.0 Serv” contains the results of the proteolytic cleavage sites of the precursors indicated in the file named “02 ACP selected EA,” which were generated using the aforementioned software. C02: BLAST VP. The folder contains the results of the BLAST alignment against the NCBI database, which were generated with the virtual peptide sequences reported by Martinez-Perez et al. (2007). This folder contains seven text files. The name of each file corresponds to the precursor and species in which it was identified. Moreover, the PDF document named “Virtual peptides ProP 1.0 Serv” contains the results of the proteolytic cleavage sites generated with the aforementioned software. C03: Debugging sequences with software. This folder contains three subfolders containing the results obtained with each software used in this study for the detection of each of the neuropeptide sequences using the appropriate keywords. The folder named “BioDataToolKit” contains six subfolders with the abbreviated name of each neuropeptide. Additionally, there is a file containing the sequences downloaded from the GenBank database, as well as a Microsoft Excel file containing the details generated by the software. The name of each file corresponds to the keywords used for each search. The software used in this study can be found in the following repository: <a href="https://github.com/rduarte24/BiodataToolkit">https://github.com/rduarte24/BiodataToolkit</a>. The folder named “Pro1.0Server” was organized in the same way as the results derived for the “BioDataToolKit” for each neuropeptide family. However, each of the neuropeptide folders contained a file with the pertinent sequences whereas another file contained the endoproteolytic cleavage sites of the neuropeptide precursors obtained with the software. The folder named “Proteios” contains seven files. The file names indicate the precursor analyzed with the software and the identified sequences in FASTA format. The Proteios software is available in the following website: <a href="https://github.com/Martin-Munive/Proteios">https://github.com/Martin-Munive/Proteios</a>. C04: Neuropeptide precursors for evolutionary analysis. Files with the sequences of the neuropeptide precursors used for the generation of the phylogenetic trees in Supplementary Materials 4 and 7. The name of each file corresponds to the name of each of the analyzed neuropeptides. R2: Transcriptome BLAST Microsoft Excel file containing the BLAST alignments conducted using the sequences of the AKH/CRZ-related peptide (ACP) from C. toxotes and Corazonin (CRZ) from C. arcuatus. The following information is summarized in the spreadsheets named C. toxotes and C. arcuatus: Column A, neuropeptide name; Column B, species name; Columns C–G, BLAST alignment results; Column H, GenBank protein accession number; Column I, precursor sequence. R3: Construction of neuropeptide database Microsoft Excel file with information pertaining to the database and a detailed description of each of the neuropeptide precursors analyzed in this study. The Excel file contains seven spreadsheet tabs. Each of the tabs contains the following columns: Neuropeptides. Column A, sequence numbering in descending order; Column B, neuropeptide name; Column C, identification code used in this study; Column D, accession number; Columns E–G, species taxonomy; Columns H–L, GenBank sequence description; Columns M–N, literature reference and link. Taxonomy. Taxonomic description of each of the examined species derived from the NCBI database. Sequences evolutionary anal. This tab contains the code developed for this work in Column C; the GenBank accession codes of each neuropeptide are summarized in Column D and species taxonomy details are summarized in Columns E y F. Table of differences. Column B shows the codes of identical sequences and Column C shows the code of the sequence selected for this study. Codes deleted. This tab contains the accession codes of the species and the species name but contains no details on the properties of the neuropeptide precursors. Sequences Paper. Neuropeptide sequences reported in previous studies that were later reported in the GenBank database. The sequences marked with asterisks have not been previously reported in public databases. The codes used in this study to designate the sequences are also included. Keywords. Keywords used to conduct the GenBank database searches to obtain the members of each neuropeptide family. R4: In silico validation, alignments, and phylogenetic relationships Generated phylogenetic trees and results obtained from individual runs for each of the neuropeptide families with the DNA-LM and Kalign parameters using the IQ-TREE software. The folder named “RUN” contains the “DNALM and kalign 2.0 default parameters” subfolder. Both folders contain 11 subfolders with the names of each of the neuropeptide families, as well as the results obtained with the IQ-TREE software. The folder named “Trees” contains the folder “DNALM and kalign 2.0 default parameters” containing the phylogenetic trees for each of the neuropeptide families, which were created with the Itol software. R5: BLAST alignment of the virtual peptide precursors Results of the BLAST alignment of the virtual peptides described by Martinez-Perez et al. (2007) with respect to the sequences in the GenBank database. The files follow the same nomenclature as in the folder named “Carpeta 02 BLAST VP” in Repository 1. R6: Alignment of neuropeptide precursors “DNALM and Kalign 2.0 default parameter” folders. Each of these folders contains the alignments of the examined neuropeptide precursors from each family and each folder is named after the corresponding neuropeptide. The remaining files contain the alignments in ascending order in the evolutionary scale and are appropriately named after the corresponding neuropeptide. The file named “All Sequence FASTA” contains the sequences used in our study in FASTA format. R7: Phylogenetic clustering of the precursors  “DNALM and Kalign 2.0 default parameter” folders. Both folders contain the phylogenetic tree clustering results from Supplementary Material 6, which were obtained using the DNA-LM y Kalign parameters and the IQ-TREE software. All analyses were conducted using the GUANE-1 supercomputer (Universidad Industrial de Santander). The phylogenetic clustering results of all of the precursors are contained in the folders with the respective precursor name. The folder also contains Figure 6, which was included in our main manuscript. Additionally, a folder entitled "Orthofinder and Robinson-Foulds" is included, which corresponds to the analyses carried out for: the Robinson-Foulds metric and the Orthofinder software.

opencc-by-4.0Aug 2023View details →

Data for: Grain structure evolution ahead of the die during friction extrusion of AA2024

Friction extrusion (FE) is a thermo-mechanical process using a rotating die to produce fully consolidated extrudates in different shapes, e.g. wires, rods and tubes. FE utilizes a non-consumable die to plastically deform material and to generate heat by friction due to the relative rotation between the die and feedstock. In this study, the FE process is applied to extrude the Al-Cu alloy AA2024 using a 90 degree scroll-featured die. The grain structure evolution induced by thermo-mechanical processing is analyzed, in particular using the electron backscatter diffraction technique. Introduction of severe plastic deformation and high temperature exposure induced by the die movement in radial and longitudinal directions relative to the materials enable grain refinement induced by dynamic recrystallization. The grain structure formation prior to deformation through the die orifice plays an essential role to obtain fully-recrystallized homogeneous wire.

opencc-by-4.0Aug 2023View details →

Data for: Microstructure evolution and texture development during production of homogeneous fine-grained aluminum wire by friction extrusion

This dataset contains the data for paper “Microstructure evolution and texture development during production of homogeneous fine-grained aluminum wire by friction extrusion” published in Materials Characterization. Abstract: This study aims to understand the microstructure evolution and texture development during friction extrusion of aluminium alloys, focusing on AA7075 as exemplary alloy system. Electron backscatter diffraction technique has been employed to obtain crystallographic data from various regions in front of the die and in the wire. It can be deduced that the combination of continuous dynamic recrystallization and geometric dynamic recrystallization mainly govern the formation of a fine-grained structure, however discontinuous dynamic recrystallization may also play a role at high temperature. The global shear deformation during the process was characterized as a simple shear deformation with dominant \(B/\overline{B}\)  simple shear texture components. The material flow is mainly driven by the in-plane shear strain and the extrusion-induced shear strain that are determined by die rotational speed and extrusion force, respectively. The in-plane shear strain strongly affects the formation of a homogeneous fine-grained microstructure in the aluminum wire. In this regard, a novel material flow model for friction extrusion has been proposed.

opencc-by-4.0Apr 2023View details →

The World Asellidae database and phylogeny: a collaborative backbone resource for comparative studies of subterranean life evolution

Supplementary material for the article "The World Asellidae database and phylogeny: a collaborative backbone resource for comparative studies of subterranean life evolution" - SI Figure 5: The World Asellidae phylogeny with credibility Intervals for the age of the nodes. Node labels of the phylogeny indicate the 95% credibility intervals of the estimated dates. - SI Table 1: Metadata for the 2093 COI sequences used in the study. - SI Table 4: Alignment of the 2093 COI sequences used for the delimitation of MOTUs. - SI Table 5: Alignment of the 424 COI sequences used for the four-gene dated phylogeny. - SI Table 6: Alignment of the 424 16S sequences used for the four-gene dated phylogeny. - SI Table 7: Alignment of the 424 FASTKD4 sequences used for the four-gene dated phylogeny. - SI Table 8: Alignment of the 424 28S sequences used for the four-gene dated phylogeny. - SI Table 9: Metadata for the DNA sequences used for the 4-gene dated phylogeny. - SI Table 11: Data on body size, sexual body size dimorphism, habitat specialization and habitat size used in comparative analyses. - SI Table 12: Metadata for the DNA sequences deposited in NCBI as part of this study.

opencc-by-4.0Sep 2023View details →

Multilevel atlas comparisons reveal divergent evolution of the primate brain

Nifti files of 20 mammalian atlases modified into a Common Multilevel Segmentation. (See Figure 1 in Multilevel atlas comparisons reveal divergent evolution of the primate brain; https://www.pnas.org/doi/full/10.1073/pnas.2202491119#sec-3) These nifti files are based on the brain atlases from 18 mammalian species, that were published between the years 2013 and 2021 (see list). The Python script to re-segment the "original" atlases into the modified version (that is shared here) is also available: see Modify_atlases.py Each species folder contains 5 nifti files: 1 for each level of segmentation and 1 for the brain segmentation. The other txt files are the volumetric output extracted using AFNI on each nifti file. Please read the Readme.txt file to credit and cite accordingly all the authors.

opencc-by-4.0Sep 2023View details →

Data from: The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

The dataset contains intermediate output files required to reproduce the figures in the main text and Supporting Material of Willink et al. 2023. The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies. FILE OVERVIEW: 1. Morph-specific assemblies     A. File names: Afem_1354_ragtag.fasta.gz, Ifem_1049_ragtag.fa.gz, Ofem_0081_ragtag.fa.gz, O054_Shasta_run2.PMDV.HAP1.purged.fasta.gz, A059_Shasta_run1.PMDV.HAP1.purged.fa.gz     B. Description: genome assemblies for different morphs of Ischnura elegans (Afem_1354, Ifem_1049, and Ofem_0081) and Ischnura senegalensis (A059 and O054), generated in this study from long-read Nanopore data using Shasta v 0.7.0 (https://github.com/paoloshasta/shasta). 2. Assembly statistics     A. File names: Assembly_statistics.csv, Assembly_statistics_sen.csv     B. Description: Completeness and quality metrics for de novo genome assemblies of I. elegans and I. senegalensis female morphs. See Fig. S1-S2. 3. Repetitive content annotation     A. File names: A1354_ragtag_RED.bed.repeats.bed.gz, Afem_Shasta1_polished_ragtag_UPPER.fa.out.gz, Ifem_Shasta2_polished_ragtag_UPPER.fa.out.gz, ioIscEleg1.1.primary_UPPER.fa.out.gz, ToL_RED.repeats.bed.gz     B. Description: Annotation of repetitive sequences in morph-specific assemblies. All morph assemblies (A, I and Darwin Tree of Life assemblies) were annotated using RepeatModeler v 2.0.1 and RepeatMasker v 1.0.93 (http://www.repeatmasker.org). The A morph and  DToL assemblies were additionally annotated using Red v 0.0.1 (https://github.com/BioinformaticsToolsmith/Red). RepeatMasker annotations were then used to estimate TE coverage. See Extended Data Fig. 4 and Fig. S7. 4. GWAS output     A. File names: A1354_ragtag_AvI.assoc_filtered.txt.gz, A1354_ragtag_AvO.assoc_filtered.txt.gz, A1354_ragtag_IvO.assoc_filtered.txt.gz, ToL_AvI.assoc_filtered.txt.gz, ToL_AvO.assoc_filtered.txt.gz, ToL_IvO.assoc_filtered.txt.gz     B. Description: filtered SNPs in pairwise association tests between morphs (n = 19 resequencing samples per morph) of I. elegans. Analyses were conducted in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/), using either the A morph assembly (Fig. 2a-b), or the Darwin Tree of Life (DToL) reference assembly (Extended Data Figure 8a-b) as mapping reference. 5. Population statistics     A. File names: Afem_pixy_30K_fst.txt.gz, A1354_30kb.Tajima.D.gz, Afem_pi_30K_pi.txt.gz, ToL_30K_fst.txt.gz, ToL_30kb.Tajima.D.gz, ToL_30K_onepop_pi.txt.gz     B. Description: Genetic differentiation (fst) between morphs, Tajima's D statistics, and nucleotide diversity across 30 kb windows of the I. elegans genome. Population statistics were computed using either the A morph assembly (Fig. 2c-e), or the DToL reference assembly (Extended Data Figure 8c-e) as mapping reference. 6. k-mer based GWAS     A. File names: AvI_kmers.fa.gz, AvO_kmers.fa.gz, OvAI_kmers.fa.gz, AvI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, AvO_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_Ifem_1049_ragtag_table.tsv.gz     B. Description: List of significant k-mers (in fasta format) in three k-mer based association analyses (n = 19 resequencing samples per morph) between morphs of I. elegans. Significant k-mers were then mapped to morph-specific assemblies using Blast v 2.22.28 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) for short sequences. We include mapping results shown in Fig. 3a-b. 7. Read-depth coverage     A. File names: reseq_coverage_norepeat_500_window.bed.gz, nano_coverage_norepeat_500_window.bed.gz, Ifem_nano_coverage_norepeat_500_window.bed.gz, Ifem_reseq_coverage_norepeat_500_window_15Mb.bed.gz, poolseq_coverage_norepeat_500_window.bed.gz, morph_coverage_norepeat_diff_500.tsv.gz, SwD_popmap     B. Description: Read depth coverage of the morph locus and a 15 mb region used to estimate baseline read depths. 19 Illumina resequencing samples, and one long-read Nanopore sample of each morph of I. elegans were mapped to both the A and I assemblies to estimate read depth. Two poolseq samples (each pool consisting of 30 females of each morph) of I. senegalensis were mapped to the A assembly of I. elegans to estimate read depth. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) across 500 bp windows after filtering windows with more than 10% repetitive content. For poolseq samples, the difference in coverage values between the A and O pools was computed across the entire genome. Sample information for resequencing samples is recorded in the file SwD_popmap. See Fig. 3c-d, 5b, and S8. 8. Assembly alignment     A. File names: nucmer_aln_Ifem_1049_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_0081_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, karyotype_AI_RagTag.csv, karyotype_AO_RagTag.csv, karyotype_AIsen_AIele.cs, karyotype_OIsen_AIele.csv     B. Description: Assembly alignments using nucmer v 4.0.0 (https://github.com/mummer4/mummer) and contig synteny for plotting using RIdeogram v 0.2.2 (https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html) in R v 4.2.2 (https://www.r-project.org/). The A morph assembly of I. elegans was aligned to the I and O morph assemblies of I. elegans and to the A and O-like assemblies of I. senegalensis. See Fig. 4a, 5c. 9. Genotyping the Darwin Tree of Life assembly     A. File names: nucmer_aln_Afem_ragtag_ToL-haplotigs.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_ragtag_ToL-primary.qr1_filter.reformat.coords.gz, ToL_500_norepeat.regions.bed.gz, karyotype_AToL_13_unloc_RagTag.csv, karyotype_AToL_RagTag_haplotigs.csv     B. Description: To genotype the DToL reference assembly of I. elegans, we estimated read-depth coverage of the DToL long-read Pacbio data mapped to the A morph assembly of I. elegans generated in this study, and aligned the A morph assembly to both the primary DToL assembly and to the purged haplotigs. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) and assembly alignments were conducted using nucmer v 4.0.0 (https://github.com/mummer4/mummer). See Fig. S3. 10. SV calling     A. File names: A_to_A.bam, A_to_A.bam.bai, A_to_I.bam, A_to_I.bam.bai, A_to_O.bam, A_to_O.bam.bai, A_to_ToL_2mb.bam, A_to_ToL_2mb.bam.bai, I_to_A.bam, I_to_A.bam.bai, I_to_I.bam, I_to_I.bam.bai, I_to_O.bam, I_to_O.bam.bai, I_to_ToL_2mb.bam, I_to_ToL_2mb.bam.bai, O_to_A.bam, O_to_A.bam.bai, O_to_I.bam, O_to_I.bam.bai, O_to_O.bam, O_to_O.bam.bai, O_to_ToL_2mb.bam, O_to_ToL_2mb.bam.bai     B. Description: mergede alignements of resequencing samples (n = 19 per morph) to alternative reference assemblies (A, I, O, and DToL) for I. elegans. The alignments have been filtered by quality and to contain only the unlocalized scaffold 2 of chromosome 13, which includes the morph locus. These files were used to call morph-specific structural variants using samplot v 1.3.0 (https://github.com/ryanlayer/samplot). See Extended Data Figs 2, 7, and Fig. S5-S6. 11. Mapping of inversion breakpoint reads     A. File names: AvO_3K.tsv.gz, AvO_22K.tsv.gz, AvO_sen_3K.tsv.gz, AvO_sen_22K.tsv.gz, IvO_3K.tsv.gz     B. Description: Signatures of an inversion with breakpoints at ~ 3 kb and ~ 22 kb of the unlocalized scaffold 2 of chromosome 13 on the O assembly were found in A and I resequencing samples of I. elegans and in poolseq samples of A females of I. senegalensis. We queried the reads mapping to the inversion breakpoints and then tabulated their mapping locations of the A morph assembly of I. elegans (Fig. 6 and Extended Data Fig. 3, 7b-c). For the first inversion breakpoint, we also mapped reads on the I morph assembly of I. elegans (Fig. S12). 12. Evidence of translocation in I     A. File names: Ifem_nano_SUPER_13_unloc_2.bam, Ifem_nano_SUPER_13_unloc_2.bam.bai     B. Description: Long-read Nanopore data of a I morph female of I. elegans mapped to the A morph of I. elegans and filtered to contain the entire unlocalized scaffold 2 of chromosome 13. Read mapping was conducted in minimap2 v 2.22-r1110 (https://github.com/lh3/minimap2) and used to identify a translocation signature in the I morph, relative to the A morph of I. elegans. See Extended Data Fig. 6. 13. PCA output     A. File names: A1354_all.eigenval, A1354_all.eigenvec, I1049_all.eigenval, I1049_all.eigenvec     B. Description: Eigenvectors and eigenvalues of PCA analyses of population structure between morphs of I. elegans. PCA analysis were conducted on morph locus, using either the A morph or the I morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Fig. S4. 14. Linkage disequilibrium     A. File names: A1354_SUPER_1_allr.ld.gz, A1354_SUPER_2_allr.ld.gz, A1354_SUPER_3_allr.ld.gz, A1354_SUPER_4_allr.ld.gz, A1354_SUPER_5_allr.ld.gz, A1354_SUPER_6_allr.ld.gz, A1354_SUPER_7_allr.ld.gz, A1354_SUPER_8_allr.ld.gz, A1354_SUPER_9_allr.ld.gz, A1354_SUPER_10_allr.ld.gz, A1354_SUPER_11_allr.ld.gz, A1354_SUPER_12_allr.ld.gz, A1354_SUPER_13_allr.ld.gz, A1354_SUPER_13_unloc_1_allr.ld.gz, A1354_SUPER_13_unloc_2_allr.ld.gz, A1354_SUPER_13_unloc_3_allr.ld.gz, A1354_SUPER_13_unloc_4_allr.ld.gz, A1354_SUPER_X_allr.ld.gz     B. Description: Estimates of recombination rate (R2) between SNPs across the first 15 mb of each chromosome and unlocalized segments of chromosome 13 of I. elegans. Recombination rates were estimated based on 57 resequencing samples and using the A morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Extended Data Fig. 5. 15. Gene annotations     A. File names: Afem_all_ragtag.gtf.gz, Afem_all_transcripts.transdecoder.genome.gff3.gz, Isen.gtf.gz     B. Description: Annotation of the A morph assembly of I. elegans using RNAseq data to assemble transcripts de novo for I. elengans and I. senegalensis in Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). Peptide sequences for the I. elegans transcripts were then predicted using Transdecoder v 5.5.0 (https://github.com/TransDecoder/TransDecoder). 16. Gene annotations in the morph locus     A. File names: gene_models_shared_trancripts_simple.csv, gene_models_shared_trancripts_simple_I.csv     B. Description: locations of exon features for genes in the morphs locus and expressed in at least one adult sample of both I. elegans and I. senegalensis. Locations are given for the A and I assemblies. See Fig. 6 and S12. 17. Gene expression     A. File names: DToL_gene_count_matrix.csv.gz, DToL_transcript_count_matrix.csv.gz, gene_count_matrix.csv.gz, transcript_count_matrix.csv.gz, Isen_gene_count_matrix.csv.gz, Isen_transcript_count_matrix.csv.gz, Iele_phenodata.csv, Isen_phenodata.csv     B. Description: Sample information (phenodata), gene and transcript count matrices for gene expression analysis. For I. elegans, gene expression was quantified on thoracic tissue of six adult females of each morph and six adult males (three sexually mature and three sexually immature in each group). Reads were mapped to both the A morph assembly and the DToL reference assembly. For I. senegalensis, we used previously published data (NCBI BioProject PRJDB11387) from different tissues of adult females of each morph and males (one upon emergence and one two days after emergence for each group) mapped to the A morph assembly. Gene and transcript counts were generated using Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). See Fig. 6, S9-S11, S13. 18. SNPs in the morph locus     A. File names: A1354-ragtag-allsites-candidate_gene_cds.vcf.gz, A1354-ragtag-allsites-candidate_gene_cds.vcf.gz.tbi, vcf_popmap     B. Description: SNPs in 57 resequencing samples across coding sequences of the morph locus of I. elegans. The A morph assembly was used as mapping reference. Sample information for resequencing samples is recorded in the file vcf_popmap. See Fig. S14a. 19. Domains and orthologues of Gastrula zinc-finger transcription factor in the morph locus     A. File names: GZnf_domain_annot.csv, GZnF_orthologue.tre, GZnf_orthologue_annot.txt     B. Description: Functional domains were annotated using InterProScan (https://www.ebi.ac.uk/interpro/). The gene orthologue tree was inferred using OrthoFinder v 2.5.2 (https://github.com/davidemms/OrthoFinder). See Fig. S14.

dryad44/100

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Open the record for dataset details and reuse information.

publicDec 2019View details →

edi44/100

Surface abrasion and crust evolution following vegetation removal at the Jornada Basin LTER Scrape Site, 1995 to 2019

This data package contains measurements of soil surface abrasion and the evolution of soil crust shear strength following a soil and vegetation removal (scrape) treatment at the Jornada Basin LTER site in southern New Mexico, USA. Soil erosion and soil crust shear strength is measured at 3 locations along the prevailing wind direction across a site initially scraped in 1995 to remove the A soil horizon in a 100 meter radius semicircle. There are three monitoring stations (East, Middle, West) on the Scrape Site. The West site is the windward site, the East site is the leeward site, and the middle site is halfway between the other two. At each location, measurements are taken of the distance of the sand surface and soil crust to a crossbar set into the soil. Three "Torvane" measurements that measure the torque (shear strength) needed to break the crust are also made at each location. These measurements were made monthly until 2014, and are made annually since 2015. The Scrape Site has now become the location for the GROWES study (JRN study IDs 511 and 523). Data collection for this study is ongoing.

openCC (other)Dec 2019View details →

opencc-by-4.0Dec 2019View details →

The SPOTS Models: A Grid of Theoretical Stellar Evolution Tracks and Isochrones For Testing The Effects of Starspots on Structure and Colors

The SPOTS Models: A Grid of Theoretical Stellar Evolution Tracks and Isochrones For Testing The Effects of Starspots on Structure and Colors This repository contains the Stellar Parameters of Tracks with Starspots (SPOTS) grid of theoretical stellar evolutionary tracks and isochrones, presented in Somers, Pinsonneault, and Cao (2020, in prep). Our models were calculated with the Yale Rotating Evolution Code (e.g. van Saders & Pinsonneault, 2013, ApJ 776, 67), including updated which incorporate a treatment of surface starspots (Somers & Pinsonneault, 2015, ApJ 807, 174S). Modelling details can be found in these references. The purpose of this evolutionary suite is to provide the community with state-of-the-art predictions for the influence of starspots and magnetic activity on the structure of stars. The grid includes both isochrones and tracks. They can be downloaded individually from this repository, or in bulk by downloading the .zip files. Isochrones (.isoc): Each isochrone file contains a series of isochrones (stellar properties for a range of masses at fixed age) for ages between 1 Myrs and 4 Gyrs. Each file contains these isochrones for a different surface starspot covering fraction, given by the name of the file --  f000.isoc = 0% covering fraction, f017.isoc = 17% covering fraction, etc. Each isochrone contains several columns with different information, including, <ol> <li>Fundamental properties: mass, age, luminosity, radius, logg, Teff, convective overturn timescale (TauCZ), lithium abundance relative to initial (Li/Li0).</li> <li>Starspot properties: Covering fraction (Fspot), ratio of spot temperature to ambient temperature (Xspot), the temperatures of hot and cool regions (T_hot, T_cool).</li> <li>Two-temperature colors, including Johnson BV, Cousins RI, 2MASS JHK, WISE W1, and Gaia G, BP, RP.</li> </ol> Colors that fell outside of the calibrated range are listed as -99.0. Tracks (.track): We also include individual tracks for every combination of Fspot and Mass considered in the paper. Each .track file lists the mass and starspot covering fraction in the filename -- i.e. m055_f034.track is the model of mass 0.55Msun and with a 34% surface covering fraction. In addition to all the properties included in the isochrones, the track files also include: <ol> <li>The total moment of interia of the model (total_I) and the moment of interia of the surface convection zone (CZ_I)</li> <li>The central and surface hydrogen abundances (X_cen, X_surf) and the surface metallicity (Z/X_surf)</li> <li>The deuterium abundance relative to initial (H2/H2_0)</li> </ol>

opencc-by-4.0Jan 2020View details →

DFT optimised structure used for the paper "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst"

DFT optimised structures used to calculate the OER activities in "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst". The structures are bundled in two databases, LiIrO3.db which contains all structures for alpha-LiIrO3 and KLiIrO3-disordered.db which contains all the structures for the disordered Li0.75K0.25(H2O)0.50IrO3 structure. The structures can be retrieved using the Atomic Simulation Environment (ASE, https://wiki.fysik.dtu.dk/ase/index.html). The keywords 'ads' and 'surface' can be used to search the structure, e.g. surface='Z-step' and ads='*OOH' will give the structure with OOH adsorbed on the Z-step surface (see paper for details on the different surfaces).

FIG. 7 in Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe

FIG. 7. — Comparison of the occlusal angle (OA) of various mammoth taxa from various localities in Europe. Data from Van Essen (2011) and obtained from illustrations from Palombo & Ferretti (2005) and Lister et al. (2005).

FIG. 3 in Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe

FIG. 3. — Dental remains of Mammuthus meridionalis vestinus (Azzaroli in Ambrosetti, Azzaroli, Bonadonna & Follieri, 1972) from Apollonia-1: A-C, left M3 fragment (APL-686B) in occlusal (A), buccal (B), and lingual (C) views; D-F, left m3 (APL-687) in occlusal (D), lingual (E), and buccal (F) views. Scale bar: 5 cm.

FIG. 2 in Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe

FIG. 2. — Right maxilla fragment with DP2-DP3 (APL-225) of Mammuthus meridionalis vestinus (Azzaroli in Ambrosetti, Azzaroli, Bonadonna & Follieri, 1972) from Apollonia-1: ventral (A), medial (B), and lateral (C) views. Scale bar: 5 cm.

FIG. 1. — A in Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe

FIG. 1. — A, Geological map and simplified composite stratigraphic column of the Neogene and Quaternary lithostratigraphic units of Mygdonia Basin, showing the location of Apollonia-1 (map and column modified from Koufos et al. [1995] and Konidaris et al. [2015]); B, hemi-mandible APL-716 in situ; C, m3 APL-687 in situ.