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Supplementary material 6 from: Agnarsson I, LeQuier SM, Kuntner M, Cheng R-C, Coddington JA, Binford G (2016) Phylogeography of a good Caribbean disperser: Argiope argentata (Araneae, Araneidae) and a new 'cryptic' species from Cuba. ZooKeys 625: 25-44. https://doi.org/10.3897/zookeys.625.8729
Table S3 : Explanation note: Genetic and Geographic distances among all ingroup specimens used in generating Figure 2.
Supplementary material 5 from: Agnarsson I, LeQuier SM, Kuntner M, Cheng R-C, Coddington JA, Binford G (2016) Phylogeography of a good Caribbean disperser: Argiope argentata (Araneae, Araneidae) and a new 'cryptic' species from Cuba. ZooKeys 625: 25-44. https://doi.org/10.3897/zookeys.625.8729
Table S2 : Explanation note: Results of Fst and Kxy (average number of nucleotide differences) analyses among specimens from all islands and mainland. The Cuban specimens, here described as a new species, stand out in both analyses indicating genetic isolation and divergence.
Supplementary material 2 from: Agnarsson I, LeQuier SM, Kuntner M, Cheng R-C, Coddington JA, Binford G (2016) Phylogeography of a good Caribbean disperser: Argiope argentata (Araneae, Araneidae) and a new 'cryptic' species from Cuba. ZooKeys 625: 25-44. https://doi.org/10.3897/zookeys.625.8729
Figure S2 : Explanation note: Bayesian phylogeny based on analysis in MrBayes using the two nuclear genes.
Supplementary material 1 from: Trytsman M, Westfall RH, Breytenbach PJJ, Calitz FJ, Van Wyk AE (2016) Diversity and biogeographical patterns of legumes (Leguminosae) indigenous to southern Africa. PhytoKeys 70: 53-96. https://doi.org/10.3897/phytokeys.70.9147
Statistical results of the clustering analysis using the Agglomerative Hierarchical Clustering method. :
Supplementary material 2 from: Iida T, Soga M, Koike S (2016) Effects of an increase in population of sika deer on beetle communities in deciduous forests. ZooKeys 625: 67-85. https://doi.org/10.3897/zookeys.625.9116
Table 2 : Explanation note: Estimated and observed values of beetle abundance at the island and lakeshore sites.
Supplementary material 5 from: Iida T, Soga M, Koike S (2016) Effects of an increase in population of sika deer on beetle communities in deciduous forests. ZooKeys 625: 67-85. https://doi.org/10.3897/zookeys.625.9116
Figure 1 : Explanation note: Species accumulation curves for carabid, carrion and dung beetles at the island (blue lines) and lakeshore sites (red lines).
Supplementary material 4 from: Trytsman M, Westfall RH, Breytenbach PJJ, Calitz FJ, Van Wyk AE (2016) Diversity and biogeographical patterns of legumes (Leguminosae) indigenous to southern Africa. PhytoKeys 70: 53-96. https://doi.org/10.3897/phytokeys.70.9147
The predominant soil phosphorus content, pH level and exchangeable sodium percentage (ESP) expressed as a percentage for southern African leguminochoria. :
Supplementary material 4 from: Iida T, Soga M, Koike S (2016) Effects of an increase in population of sika deer on beetle communities in deciduous forests. ZooKeys 625: 67-85. https://doi.org/10.3897/zookeys.625.9116
Table 4 : Explanation note: Estimated and observed values of beetle diversity (Shannon-Wiener diversity index) at the island and lakeshore sites.
Supplementary material 3 from: Trytsman M, Westfall RH, Breytenbach PJJ, Calitz FJ, Van Wyk AE (2016) Diversity and biogeographical patterns of legumes (Leguminosae) indigenous to southern Africa. PhytoKeys 70: 53-96. https://doi.org/10.3897/phytokeys.70.9147
The predominant mean annual rainfall and minimum and maximum temperatures expressed as a percentage for southern African leguminochoria. :
Supplementary material 1 from: Estupiñán RA, Ferrari SF, Gonçalves EC, Barbosa MSR, Vallinoto M, Schneider MPC (2016) Evaluating the diversity of Neotropical anurans using DNA barcodes. ZooKeys 637: 89-106. https://doi.org/10.3897/zookeys.637.8637
Data on the specimens examined in the present study : Explanation note: Please note that some of the sequences used in the study are incompletely referenced in the GenBank barcode database because they lack some data and we are unable to rectify this because the samples were collected too long ago (1980s or before) for the missing data to be found.
Supplementary material 4 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment with the SRP RNA sequences of Dumesic et al. (2015; Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum) aligned to our newly generated ITS sequences of Russula and Lactarius.
Supplementary material 2 from: Wahlberg N, Peña C, Ahola M, Wheat CW, Rota J (2016) PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. ZooKeys 596: 129-141. https://doi.org/10.3897/zookeys.596.8399
Sequences used for designing primers : Explanation note: A zip-file containing reference sequences for all 48 gene regions used for designing primers.
Supplementary material 1 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
COI DNA sequences obtained for Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. and Ferrisia kaki Kaydan & Pacheco da Silva, sp. n. : Explanation note: This supplementary file contais the senquences of a fragment from the mitochondrial region of Cytochrome Oxidase Subunit I of two new species of mealybugs found on persimmon trees in Southern Brazil, Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. and Ferrisia kaki Kaydan & Pacheco da Silva, sp. n.
Supplementary material 1 from: Maes D, Vanreusel W, Herremans M, Vantieghem P, Brosens D, Gielen K, Beck O, Van Dyck H, Desmet P, Vlinderwerkgroep Natuurpunt (2016) A database on the distribution of butterflies (Lepidoptera) in northern Belgium (Flanders and the Brussels Capital Region). ZooKeys 585: 143-156. https://doi.org/10.3897/zookeys.585.8019
A database on the distribution of butterflies (Lepidoptera) in northern Belgium (Flanders and the Brussels Capital Region) : Explanation note: The supplementery material provides 1) a list of published entomological references that were checked for occurrence data and 2) a list of references that used data described in this paper.
Supplementary material 1 from: Monteiro M, Reino L, Melo M, Beja P, Bastos-Silveira C, Ramos M, Rodrigues D, Neves IQ, Consciência S, Figueira R (2016) The collection of birds from São Tomé and Príncipe at the Instituto de Investigação Científica Tropical of the University of Lisbon (Portugal). ZooKeys 600: 155-167. https://doi.org/10.3897/zookeys.600.7899
Species lists referred in Tables 1 and 2 showing correspondence between scientific and common names between IOC and BirdLife Internaction/IUCN nomenclatures : Explanation note: Nomenclatural differences between International Ornithological Council and BirdLife International/IUCN lists (2016) for endemic species and endemic subspecies of São Tomé and Príncipe.
Supplementary material 1 from: DiDomenico A, Hedin M (2016) New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands. ZooKeys 586: 1-36. https://doi.org/10.3897/zookeys.586.7832
Supplementary Tables 1–3 Table S1. Voucher and locality data Table S2. PCR primer and reaction information Table S3. GenBank accession information : Explanation note:
Supplementary material 1 from: Wahlberg N, Peña C, Ahola M, Wheat CW, Rota J (2016) PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. ZooKeys 596: 129-141. https://doi.org/10.3897/zookeys.596.8399
Table S1 : Explanation note: Details of the success of sequencing of the new gene regions. GenBank accession number indicates successful sequencing, dash indicates unsuccessful amplification.
Supplementary material 2 from: Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal. Research Ideas and Outcomes 2: e8424. https://doi.org/10.3897/rio.2.e8424
An example of how amanuens.is could combine ContentMine and Hypothes.is technologies to discover information about the Zika vector Aedes aegypti and the symbiont bacterium Wolbachia.
Supplementary material 3 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
ITS/SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment comprising the 63 public ITS1 sequences with SRP RNA found in them, the three newly generated sequences, and the SRP RNA sequences from Dumesic et al. (2015) (Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum).
Supplementary material 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Full information and metadata about the genomic and metagenomic samples : Explanation note: Detailed information about metadata, DNA quality and genomic/metagenomic results of fruit-body and EcM root tip samples.
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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.