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Figure 12 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 12 Phylogenetic relationships of Macropodia spp. based on partial sequence of the COI gene, obtained using Bayesian inference. Tips of the tree colored according to their morphological identification. Numbers above the branches are the posterior probabilities.
Figure 10 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 10 Natural habitats of Macropodiz czernjawskii in the Black Sea. a, b. Male (ZMMU Ma 3549) in Cystoseira sp., on rock, Tuaphat coastal rock masif, near Gelendzhik. c. Male (ZMMU Ma 3547), on sand, of Blagoveschenskaya village, near Anapa. d. Specimen collected of Blagoveschensakya in aquarium, decorated with red algae after few days of keeping. e. A characteristic biotope of M. czernjawskii in Tuaphat. f. Biotope in Kazachya Cove, Crimean Peninsula where M. czernjawskii has been repeatedly observed. Photographs by SE Anosov.
Figure 1 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 1 Study area and the original records of Macropodia czernjawskii in the Black Sea presented in this study.
Figure 11 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 11 Estimates of evolutionary divergence over sequence pairs within and between species of Macropodia (M. czernjawskii; M. rostrata – M. parva; M. tenuirostris – M. longipes; the latter two pairs and M. parva, M. rostrata – Macropodia sp. are indicated as "?", meaning their possible conspecificity); and between genera of Majoidea. The number of base substitutions per site from averaging over all sequence pairs between groups are shown. Analyses were conducted using the Kimura 2-parameter mode. For values of K2P see also Table 3.
Supplementary material 1 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Table S1
Data from: A practical introduction to microbial molecular ecology through the use of isolation chips
In the context of anti-microbial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a four year undergraduate Masters Programme in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness / diversity indices as well as principal coordinates analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips (iChips) facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.
Data from: Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination
Knowledge on the trophic interactions among predators and their prey is important in order to understand ecology and behaviour of animals. Traditionally studies on the diet composition of insectivorous bats have been based on the morphological identification of prey remains, but the accuracy of the results has been hampered due to methodological limitations. Lately, the DNA metabarcoding and High Throughput Sequencing (HTS) techniques have changed the scene since they allows prey identification to the species level, ultimately giving more precision to the results. Nevertheless, the use of one single primer set to amplify faecal DNA produces biases in the assessed dietary composition. Three horseshoe bats overlap extensively in their distribution range in Europe: Rhinolophus euryale, R. hipposideros and R. ferrumequinum. In order to achieve the deepest insight on their prey list we combined two different primers. Results showed that the used primers were complementary at the order and species levels, only 22 out of 135 prey species being amplified by both. The most frequent prey of R. hipposideros belonged to Diptera and Lepidoptera, to Lepidoptera in R. euryale, and Lepidoptera, Diptera and Coleoptera in R. ferrumequinum. The three bats show significant resource partitioning, since their trophic niche overlap is not higher than 34%.
FIGURE 6 in A revision of the genus Conicofrontia Hampson (Lepidoptera, Noctuidae, Apameini, Sesamiina), with description of a new species: new insights from morphological, ecological and molecular data
FIGURE 6. Distribution map of sampled Conicofrontia and Hygrostola specimens.
FIGURE 1 in A revision of the genus Conicofrontia Hampson (Lepidoptera, Noctuidae, Apameini, Sesamiina), with description of a new species: new insights from morphological, ecological and molecular data
FIGURE 1. Adults of Conicofrontia species (C. bipartita and C. diamesa). Scale bar = 10 mm.
FIGURE 2 in A revision of the genus Conicofrontia Hampson (Lepidoptera, Noctuidae, Apameini, Sesamiina), with description of a new species: new insights from morphological, ecological and molecular data
FIGURE 2. Adults of Conicofrontia species (C. lilomwa and C. sesamoides). Scale bar = 10 mm.
FIGURE 4 in A revision of the genus Conicofrontia Hampson (Lepidoptera, Noctuidae, Apameini, Sesamiina), with description of a new species: new insights from morphological, ecological and molecular data
FIGURE 4. Last instar larvae of Conicofrontia species. Scale bar = 10 mm.
FIGURE 4 in Morphological and molecular evidence for a new species of freshwater crab of the genus Sudanonautes Bott, 1955 (Brachyura: Potamoidea: Potamonautidae) from Cameroon, with notes on its ecology
FIGURE 4. Habitat of Sudanonautes tiko n. sp. at Edea, Cameroon.
Figure 8 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 8 Basidiomata of Cyanosporus subungulatus (Holotype, Cui 18046). Scale bar: 10 mm. The upper figure is the upper surface and the lower figure is the lower surface of the basidiomata.
Figure 6 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 6 Basidiomata of Cyanosporus rigidus (Holotype, Cui 17032). Scale bar: 1.5 cm. The upper figure is the upper surface and the lower figure is the lower surface of the basidiomata.
Figure 4 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 4 Basidiomata of Cyanosporus flavus (Holotype, Cui 18547). Scale bar: 1 cm. The upper figure is the upper surface and the lower figure is the lower surface of the basidiomata.
Figure 11 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 11 Microscopic structures of Cyanosporus tenuicontextus (Holotype, Cui 16280) a basidiospores b basidia and basidioles. c cystidioles d hyphae from trama e hyphae from context. Drawings by: Shun Liu.
Figure 10 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 10 Basidiomata of Cyanosporus tenuicontextus (Holotype, Cui 16280). Scale bar: 1 cm. The upper figure is the upper surface and the lower figure is the lower surface of the basidiomata.
Figure 3 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 3 Maximum likelihood tree illustrating the phylogeny of Cyanosporus and its related genera in the antrodia clade based on the combined sequences dataset of ITS+nLSU+nSSU+mtSSU+RPB1+RPB2+TEF. Branches are labelled with maximum likelihood bootstrap higher than 50%, parsimony bootstrap propwortions higher than 50% and Bayesian posterior probabilities more than 0.90 respectively. Bold names = New species.
Figure 2 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 2 Maximum likelihood tree illustrating the phylogeny of Cyanosporus and its related genera in the antrodia clade based on the combined sequences dataset of ITS+TEF. Branches are labelled with maximum likelihood bootstrap higher than 50%, parsimony bootstrap proportions higher than 50% and Bayesian posterior probabilities more than 0.90 respectively. Bold names = New species.
Figure 7 from: Liu S, Xu T-M, Song C-G, Zhao C-L, Wu D-M, Cui B-K (2022) Species diversity, molecular phylogeny and ecological habits of Cyanosporus (Polyporales, Basidiomycota) with an emphasis on Chinese collections. MycoKeys 86: 19-46. https://doi.org/10.3897/mycokeys.86.78305
Figure 7 Microscopic structures of Cyanosporus rigidus (Holotype, Cui 17032) a basidiospores b basidia and basidioles c hyphae from trama d hyphae from context. Drawings by: Shun Liu.
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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.