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Data and code for Freshwater corridors in the conterminous US: a coarse-filter approach based on lake-stream networks
<p>This repository contains various datasets used to map and analyze freshwater connectivity (i.e., corridors) in the conterminous US based on networks of lakes, streams and rivers. We considered lake-stream networks as analogous to habitat corridors. Hub lakes are individual lakes that are disproportionately important for maintaining intact networks. We also analyzed the protection status of freshwater connectivity using the US Protected Areas Database v. 2.0. R analysis scripts can also be found in this repository. Much of the data we used came from published or soon-to-be published sources, which are referenced below.</p>
Imperial Robotics Lab- Lake Vrana Freshwater Dataset
<p>Raw bird diversity data and soundscape index data extracted from acoustic data and used for the analysis of acoustic diversity and bird diversity. R scripts are included for PCA , bird composition and soundscape analysis.</p>
Fig. 6 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 6. Maximum likelihood (ML) phylogenetic tree based on SSU rDNA sequences showing the position of Aponotohymena isoaustralis n. sp. using GTR + I + G as nucleotide substitution model. The new sequence from the present study is indicated by bold font (arrow). Numbers at nodes are bootstrap values from ML and the posterior probabilities from BI. Accession numbers are provided after species names. Clades representing different orders of the subclass stichotrichia are shaded. "–" at the nodes indicate disagreement between the two methods. The scale bar corresponds to 0.01 expected substitutions per site.
Fig. 5 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 5. Line diagrams and photomicrographs of Aponotohymena isoaustralis n. sp. showing morphogenetic stages on the dorsal surface after protargol impregnation. A, C – within row dorsal primordia formation for proter and opisthe with posterior thickening to form caudal cirri (arrows); B, D – unequal split of the third dorsal primordia (arrows); caudal cirri formed in 2 + 2 + 3 pattern (double arrows) at the ends of DK for proter and opisthe. Scale bar: 20 µm.
Fig. 4 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 4. Photomicrographs showing morphogenetic stages on ventral surface of protargol impregnated cells of Aponotohymena isoaustralis n. sp. A, B – de novo origin of OP (arrowheads); C – POVC (arrowheads) not contributing to OP; D – dissagregation of V/4 and V/3 (arrowhead), movement of kinetosomes from OP to anterior region of the cell (arrow); E – elongation of two primary primordia (arrowhead), kinetosomes moved from OP to contribute in the formation of IIp (arrow); F – splitting of primary primordia (arrowhead), composite origin of IIp from OP and cirrus II/2 (arrow); G – primordia Vp and VIp (arrowhead) formed from splitting of primary primordia; H – full complement of 6 FVT primordia (arrowheads); I – differentiation of new FVT cirri (arrowhead); J – newly formed DMs on the ventral surface (arrowhead); K – cell in cytokinesis. OP – oral primordium. Scale bar: 20 µm.
Fig. 3 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 3. Line diagrams showing morphogenetic stages on ventral surface of protargol impregnated cells of Aponotohymena isoaustralis n. sp. A, B – origin of OP apokinetally between the LMC and POVC for the opisthe; C – reorganization of parental UM (arrow), disaggregation of II/2 (arrowhead), III/2 (double arrowhead) and V/4 (double arrow) to form primordia IIp, IIIp and Vo respectively, kinetosomes from OP form primordia Io and IIo; D – dissagregation of IV/3 to form primordium IVp (arrow); kinetosomes from OP move anteriorly (arrowhead); the two primary primordia, one each formed from disaggregation of V/4 and V/3 split transversely (double arrow) to form primordia V and VI for proter and opisthe; E – full complement of 6 FVT primordia Ip to VIp (arrowhead) and Io to VIo (double arrowhead); F – within-row marginal primordia formation for RMC (arrowheads) and LMC (double arrowheads); G – differentiation of cirri in 1, 3, 3, 3, 4, 4 pattern; H – late divider showing formation of new dorsomarginals (arrowheads) close to newly formed RMC. LMC – left marginal cirri; OP – oral primordium. Scale bar: 20 µm.
Fig. 2 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 2. Line diagrams showing protargol impregnated vegetative cells of Aponotohymena isoaustralis n. sp. A – ventral surface; B – dorsal surface. AZM – adoral zone of membranelles, CC – caudal cirri, DK1–4 – dorsal kineties, DM1, 2 – dorsomarginals, EM – endoral membrane, LMC – left marginal cirri, PM – paroral membrane, RMC – right marginal cirri, II/2 – buccal cirri, I/1, II/3, III/3 – frontal cirri, VI/4, VI/3, IV/3, III/2 – frontoventral cirri, – IV/2, V/4, V/3 – postoral ventral cirri, V/2 and VI/2 – pretransverse ventral cirri, II/1, III/1, IV/1, V/1, VI/1 – transverse cirri. Scale bar: 20 µm.
Fig. 1 in Taxonomic and Morphogenetic Description of the Freshwater Ciliate Aponotohymena isoaustralis n. sp. (Ciliophora; Oxytrichidae) Isolated from Sanjay Lake, Delhi, India
Fig. 1. Photomicrographs of live (A, B, E, F, G, H, J, K), protargol impregnated (C, D, I, L, M) and Feulgen stained (N) cells of Aponotohymena isoaustralis n. sp. A, B – cells in ventral view; C – ventral view of a vegetative cell with 5 transverse cirri arranged in a pseudo row (arrow); D – dorsal view of a vegetative cell; E – ventral view to show the arrangement of cortical granules (arrowheads) and colou- ration; F, G and H – ventral view of different cells showing flexible body; I – anterior portion of the dorsal surface showing dorsal rows (arrowhead); J – anterior portion of the cell showing contractile vacuole (arrowhead); K – cyst; L – anterior hook (arrowhead) of paroral membrane; M – dorsal view showing caudal cirri (2 + 2 + 3) (arrowheads); N – two macronuclei. AZM – adoral zone of membranelles, LMC – left marginal cirri, RMC – right marginal cirri. Scale bars: 20 µm.
Data from: Thermal response of freshwater ciliates: can they survive at elevated lake temperatures?
<p>The response of the single-celled ciliates to increased temperature during global warming is critical for the structure and functioning of freshwater food webs. I conducted a meta-analysis of the literature from field studies and experimental evidence to assess the parameters characterising the thermal response of freshwater ciliates. The shape of the thermal performance curve predicts the ciliates' survival at supraoptimal temperatures (i.e., the width of the thermal safety margin, TSM). The ciliates' typical TSM is ~5°C. One-third of the freshwater ciliates dwelling permanently or occasionally in the pelagial cannot survive at temperatures exceeding 30°C. Likewise, cold-stenothermic species, which represent a significant fraction of euplanktonic ciliates, cannot survive by evolutionary adaptation to rapidly warming environments. The statistical analysis revealed that the ciliates' thermal performance is affected by their planktonic lifestyle (euplanktonic versus tychoplanktonic), ability to form cysts, and nutritional ecology. Bactivorous ciliates have the widest temperature niche, and algivorous ciliates have the narrowest temperature niche. Phenotypic plasticity and genetic variation, favouring the selection of pre-adapted species in a new environment, are widespread among freshwater ciliates. However, the lack of evidence for the temperature optima and imprecisely defined tolerance limits of most species hamper the present analysis. The extent of acclimation and adaptation requires further research with more ciliate species than the few chosen thus far. Recent eco-evolutionary experimental work and modelling approaches demonstrated that the ciliates' thermal responses follow general trends predicted by the metabolic theory of ecology and mechanistic functions inherent in enzyme kinetics. The present analysis identified current knowledge gaps and avenues for future research that may serve as a model study for other biota. Thermal adaptation may conflict with adaptation to other stressors (predators, food availability, pH), making general predictions on the future role of freshwater ciliates in a warmer environment difficult, if not impossible, at the moment.</p>
Figure 3 in The ecology of freshwater bivalves in the Lake Sapanca basin, Turkey
Figure 3. Length–frequency distribution of (a) Unio crassus, (b) Unio pictorum, (c) Anodonta anatina, (d) Anodonta cygnea in the Lake Sapanca basin.
Figure 2 in An alien species or another perspective to the freshwater gobies puzzle: a new finding in Lake Prespa
Figure 2. Economidichthys pygmaeus from Lake Prespa (a), and the perianal organ of one of the specimens (b).
Figure 1 in An alien species or another perspective to the freshwater gobies puzzle: a new finding in Lake Prespa
Figure 1. Distribution of Economidichthys sp. in western Greece (a) the location of Lake Prespa, and the sampling sites (b).
Figure 1 in First record of the occurrence of the Chinese pond mussel Sinanodonta woodiana (Lea, 1834) (Bivalvia: Unionidae) in African freshwaters: Oubeira Lake, Algeria
Figure 1. Location of Oubeira Lake in the boundaries of El-Kala National Park (modified from Sarri, 2017).
Figure 3 in First record of the occurrence of the Chinese pond mussel Sinanodonta woodiana (Lea, 1834) (Bivalvia: Unionidae) in African freshwaters: Oubeira Lake, Algeria
Figure 3. Scheme of measurements for S. woodiana from Oubeira Lake (photos by Bensaâd-Bendjedid L.): shell's length (SL), height (SH), and width (SW).
Fig. 3 in Caridina Spongicola, New Species, A Freshwater Shrimp (Crustacea: Decapoda: Atyidae) From The Ancient Malili Lake System Of Sulawesi, Indonesia
Fig. 3. Caridina spongicola, new species, paratype female (cl 2.6 mm) (ZMB 29027), Lake Towuti, Sulawesi. A, cephalothorax and cephalic appendages; lateral view; B, mandible; C, maxillule; D, first maxilliped; E, third maxilliped; F, second maxilliped; G, maxilla; H, male first pleopod; paratype male (cl 1.9 mm) (ZMB 29027); I, male second pleopod; paratype male (cl 1.9 mm) (ZMB 29027). Scale bars: A = 1 mm; B-G = 0.5 mm; H, I = 0.2 mm.
Fig. 1. A in Caridina Spongicola, New Species, A Freshwater Shrimp (Crustacea: Decapoda: Atyidae) From The Ancient Malili Lake System Of Sulawesi, Indonesia
Fig. 1. A, Malili Lake system of Sulawesi: Caridina spongicola, new species, collecting sites in the outlet bay of Lake Towuti; B, rostrum variation within a population of C. spongicola (ZMB 29027) (scale bar: 1 mm); C, Caridina spongicola in its natural habitat; D, colour pattern of C. spongicola (ZMB).
Fig. 2 in Caridina Spongicola, New Species, A Freshwater Shrimp (Crustacea: Decapoda: Atyidae) From The Ancient Malili Lake System Of Sulawesi, Indonesia
Fig. 2. Caridina spongicola, new species, paratype female (cl 2.1mm) (ZMB 29027), Lake Towuti, Sulawesi: A, cephalothorax and cephalic appendages, lateral view; B, preanal carina; C, dactylus of third pereiopod; D, third pereiopod; E, telson; F, uropodal diaeresis; G, dactylus of fifth pereiopod; H, fifth pereiopod; I, distal end of telson; J, first pereiopod, K, second pereiopod; L, SEM images of chela and carpus of first and second pereiopods. Scale bars: A = 1 mm; B, D, H-M = 0.5 mm; C, F-G = 0.2 mm.
Figure 2 in Protozoan ciliate epibionts on the freshwater shrimp Caridina (Crustacea, Decapoda, Atyidae) from the Malili lake system on Sulawesi (Indonesia)
Figure 2. (a) Acineta; (b) Thuricola; (c) Cothurnia; (d) Vorticella; (e) Opercularia; (f) Zoothamnium. l, lorica; ma, macronucleus; mi, micronucleus; my, myoneme; o, operculum; s, stalk; sa, suprastylar area; t, tentacles.
Figure 1 in Protozoan ciliate epibionts on the freshwater shrimp Caridina (Crustacea, Decapoda, Atyidae) from the Malili lake system on Sulawesi (Indonesia)
Figure 1. The Malili lake system on the Indonesian island of Sulawesi with its three main lakes: Lake Towuti, Lake Mahalona, and Lake Matano.
Figure 24 in Epibiontic communities on the freshwater shrimp Caridina ensifera (Crustacea, Decapoda, Atyidae) from Lake Poso (Sulawesi, Indonesia)
Figure 24. Distribution of each epibiont species (mean densities) along the anterioposterior axis of Caridina ensifera. Anatomical units are considered individually. per, pereiopod; ple, pleopod; uro, uropod.
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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.