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Supplementary material 2 from: Garcia Rodrigues J, Conides A, Rivero Rodriguez S, Raicevich S, Pita P, Kleisner K, Pita C, Lopes P, Alonso Roldán V, Ramos S, Klaoudatos D, Outeiro L, Armstrong C, Teneva L, Stefanski S, Böhnke-Henrichs A, Kruse M, Lillebø A, Bennett E, Belgrano A, Murillas A, Sousa Pinto I, Burkhard B, Villasante S (2017) Marine and Coastal Cultural Ecosystem Services: knowledge gaps and research priorities. One Ecosystem 2: e12290. https://doi.org/10.3897/oneeco.2.e12290
Correspondence between our classification and labels for marine and coastal CES as found in the literature
Supplementary material 1 from: Chen C-W, Sundue M, Kuo L-Y, Teng W-C, Huang Y-M (2017) Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae. PhytoKeys 78: 83-107. https://doi.org/10.3897/phytokeys.78.12040
Figure S1. Maximum likelihood phylogram of Polypodiineae obtained from the combined (rbcL + rps4-trnS + trnL-F) dataset. : Explanation note: Maximum likelihood bootstrap percentages (BS) are provided at each node. Thickened lines indicate Bayesian inference posterior probability (PP) ≥ 0.9.
Supplementary material 4 from: Chen C-W, Sundue M, Kuo L-Y, Teng W-C, Huang Y-M (2017) Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae. PhytoKeys 78: 83-107. https://doi.org/10.3897/phytokeys.78.12040
Figure S4. Maximum likelihood phylogram of Polypodiineae obtained from the trnL-F dataset. : Explanation note: Maximum likelihood bootstrap percentages (BS) are provided at each node. Thickened lines indicate Bayesian inference posterior probability (PP) ≥ 0.9.
Supplementary material 3 from: Chen C-W, Sundue M, Kuo L-Y, Teng W-C, Huang Y-M (2017) Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae. PhytoKeys 78: 83-107. https://doi.org/10.3897/phytokeys.78.12040
Figure S3. Maximum likelihood phylogram of Polypodiineae obtained from the rps4-trnS dataset. : Explanation note: Maximum likelihood phylogram of Polypodiineae obtained from the rps4-trnS dataset. Maximum likelihood bootstrap percentages (BS) are provided at each node. Thickened lines indicate Bayesian inference posterior probability (PP) ≥ 0.9.
Supplementary material 2 from: Jeppson M, Altés A, Moreno G, Nilsson RH, Loarce Y, de Bustos A, Larsson E (2017) Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma (Agaricales). MycoKeys 21: 33-88. https://doi.org/10.3897/mycokeys.21.12176
Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma : Explanation note: Distance matrices of the ITS alignment (uncorrected "p" distance and GTR distance) and the multiple sequence alignmnet of the ITS.
Supplementary material 2 from: Chen C-W, Sundue M, Kuo L-Y, Teng W-C, Huang Y-M (2017) Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae. PhytoKeys 78: 83-107. https://doi.org/10.3897/phytokeys.78.12040
Figure S2. Maximum likelihood phylogram of Polypodiineae obtained from the rbcL dataset. : Explanation note: Maximum likelihood bootstrap percentages (BS) are provided at each node. Thickened lines indicate Bayesian inference posterior probability (PP) ≥ 0.9.
Supplementary material 1 from: Jeppson M, Altés A, Moreno G, Nilsson RH, Loarce Y, de Bustos A, Larsson E (2017) Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma (Agaricales). MycoKeys 21: 33-88. https://doi.org/10.3897/mycokeys.21.12176
Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma : Explanation note: Data of specimens sequenced in this study with GenBank accession numbers for the ITS/LSU and TEF-1α regions. Type specimens are marked in bold.
Supplementary material 1 from: Kadej M, Zając K, Smolis A, Tarnawski D, Tyszecka K, Malkiewicz A, Pietraszko M, Warchałowski M, Gil R (2017) The great capricorn beetle Cerambyx cerdo L. in south-western Poland – the current state and perspectives of conservation in one of the recent distribution centres in Central Europe. In: Campanaro A, Hardersen S, Sabbatini Peverieri G, Carpaneto GM (Eds) Monitoring of saproxylic beetles and other insects protected in the European Union. Nature Conservation 19: 111-134. https://doi.org/10.3897/natureconservation.19.11838
Table S1. Correlation matrix of all initial environmental layers selected for modelling in MaxEnt : Data type: statistical data
Supplementary material 1 from: Seidel M, Jameson ML, Stone RL (2017) A new cryptic species and review of the east-Andean leaf chafer genus Mesomerodon Ohaus, 1905 (Coleoptera, Scarabaeidae, Rutelinae). ZooKeys 671: 61-85. https://doi.org/10.3897/zookeys.671.11815
Distribution data for Mesomerodon species (Coleoptera, Scarabaeidae, Rutelinae) : Explanation note: Specimen level data used for niche model, phenology, and overall distribution.
Supplementary material 3 from: Okanishi M, Fujita T, Maekawa Y, Sasaki T (2017) Non-destructive morphological observations of the fleshy brittle star, Asteronyx loveni using micro-computed tomography (Echinodermata, Ophiuroidea, Euryalida). ZooKeys 663: 1-19. https://doi.org/10.3897/zookeys.663.11413
Figure S3 : Explanation note: The interactive 3D model of µ CT surface rendering images of the isolated vertebral ossicles of Asteronyx loveni (NSMT E-5638).
Supplementary material 2 from: Okanishi M, Fujita T, Maekawa Y, Sasaki T (2017) Non-destructive morphological observations of the fleshy brittle star, Asteronyx loveni using micro-computed tomography (Echinodermata, Ophiuroidea, Euryalida). ZooKeys 663: 1-19. https://doi.org/10.3897/zookeys.663.11413
Figure S2 : Explanation note: The interactive 3D model of µ CT surface rendering images of the basal part of an arm of Asteronyx loveni (NSMT E-5638).
Supplementary material 1 from: Okanishi M, Fujita T, Maekawa Y, Sasaki T (2017) Non-destructive morphological observations of the fleshy brittle star, Asteronyx loveni using micro-computed tomography (Echinodermata, Ophiuroidea, Euryalida). ZooKeys 663: 1-19. https://doi.org/10.3897/zookeys.663.11413
Figure S1 : Explanation note: The interactive 3D model of µ CT surface rendering images of the entire body of Asteronyx loveni (NSMT E-6986). This image can be activated by clicking on the image in Adobe Acrobat Reader (version 8 or higher) and can be rotated, moved and magnified.
Supplementary material 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Common OTU lists and Statistical analysis : Explanation note: This file contains detected OTUs in both methods and biodiversity analysis (GLM and t-test)
Supplementary material 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Biodiversity workflow in R : Explanation note: Bundle of files for biodiversity analysis in R. All necessary input files and a commented script of R-commands are provided.
Supplementary material 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Master data sheet : Explanation note: Spreadsheet file containing information about read abundances of operational taxonomic units (OTUs) and sample metadata. Here, data were prepared for subsequent biodiversity analysis in R.
Supplementary material 1 from: Leijs R, Batley M, Hogendoorn K (2017) The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: A revision of the subgenera Notomegilla and Zonamegilla. ZooKeys 653: 79-140. https://doi.org/10.3897/zookeys.653.11177
Phylogenetic trees and table of DNA voucher numbers, including Genbank accession numbers : Explanation note: Figure S1. CO1 (primers M70/M202) neighbour-joining tree calculated using uncorrected sequence divergence in PAUP*. Terminals are labelled with RB-numbers, which refer to Table S1, sequencing primer or 'cons', indicating consensus sequence based on forward and reverse sequencing.
Supplementary material 2 from: Leijs R, Batley M, Hogendoorn K (2017) The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: A revision of the subgenera Notomegilla and Zonamegilla. ZooKeys 653: 79-140. https://doi.org/10.3897/zookeys.653.11177
Examined specimens : Explanation note: The database contains information copied from specimen labels for each species: including repository, catalogue numbers and DNA voucher numbers.
Supplementary material 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265
Bioinformatics pipeline : Explanation note: This file provides all steps and commands necessary for quality filtering and demultiplexing of raw paired fastq sequences.
Supplementary material 1 from: Visagie CM, Yilmaz N, Renaud JB, Sumarah MW, Hubka V, Frisvad JC, Chen AJ, Meijer M, Seifert KA (2017) A survey of xerophilic Aspergillus from indoor environment, including descriptions of two new section Aspergillus species producing eurotium-like sexual states. MycoKeys 19: 1-30. https://doi.org/10.3897/mycokeys.19.11161
Species isolated from house dust using selective xerophilic media : Explanation note: Species isolated from house dust using selective xerophilic media, their occurrence and GenBank numbers for sequences generated for these strains.
Supplementary material 3 from: Machado A, Rodríguez-Expósito E, López M, Hernández M (2017) Phylogenetic analysis of the genus Laparocerus, with comments on colonisation and diversification in Macaronesia (Coleoptera, Curculionidae, Entiminae). ZooKeys 651: 1-77. https://doi.org/10.3897/zookeys.651.10097
Chronogram of genus Laparocerus Schönherr, 1834 from Macaronesia (Coleoptera, Curculionidae, Entiminae) : Explanation note: Timetree generated with MEGA7 (Kumar et al. 2016) using the RelTime method. Divergence times for all branching points in the Bayesian phylogram (COII, 16S rRNA, 12S rRNA) calculated using Maximum Likelihood method with the General Time Reversible model. Relative times were optimized and converted to absolute divergence times (shown next to branching points) based on not allowing species cluster marked with ♦ to be older than the age of the island of La Palma (1,72 Ma) or younger than 0.21 Ma. Bars around each node represent 95% confidence intervals which were computed using the method described in Tamura et al. (2013). The estimated log likelihood value is -32807.3327. A discrete gamma distribution was used to model evolutionary rate differences among sites (6 categories (+G, parameter = 0.5622)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 42.7318% sites). The analysis involved 255 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1357 positions in the final dataset. Taxon codes include an abbreviation of species name, its code number, and the initial of the island of origin (see Appendix 1).
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.