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14,185 results for “phylogenies”
Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser
<p>In our publication, we created simulations of paired heavy and light chain BCR sequences. Uploaded here is all the data needed to rerun the simulations, as well as the output of the simulations we ran. The output of BCR phylo included here are the lineage trees, unpickled and put into one file (true_trees.tsv), and the fasta files ('starting_fastas' folder). The naive BCR sequences we used as a starting point are found in the 'naive_data' folder. The post-simulation data for all 20 iterations (combined heavy and light chain data through both simulation frameworks) can be found in the 'simulation_data' folder.</p>
figure 4 in Infirm effect of phylogeny on morphometric features in a cryptic Gobio species complex
figure 4 Relations of pairwise morphometric differences and geographic distances of the studied five populations (results of pairwise Mantel-tests, using 9999 permutations) in case of the three morphometric methods used (gmb: Geometric Morphometry of Body, gms: Geometric Morphometry of Scales, dbm: Distance Based Method). The equations and correlation values refer to the linear trend line.
figure 2 in Infirm effect of phylogeny on morphometric features in a cryptic Gobio species complex
figure 2 Results of phylogenetic analyses using mtCR sequence data of 102 Carpathian gudgeon individuals. Maximum likelihood tree showing the divergence of the eight haplotypes derived from the 608 bp long sequence data. Outgroup: Romanogobio vladykovi (Fang, 1943) GenBank acc. number: mk 975878. Bootstrap support values are shown next to the branches (A). PCoA plot derived from the pairwise nucleotide differences of haplotypes. The attributed variance in each axis is indicated in parentheses (B). Median-Joining network of mtCR sequence data (C). Circle sizes are relative to the number of individuals carrying the same haplotype. Line length refers to the genetic distances of haplotypes. Colour codes of cryptic groups on subfigures A, B and C are identical and correspond with figs 1 and 3 (Blue: G. obtusirostris, red: southern haplogroup, Green: G. sp1). Different colours on subfigure "C" represents different populations. Light Green: Pop1, Brown: Pop2, Orange: Pop3, Black: Pop4, Light Blue: Pop5). For more details, see fig. 1 and table 1.
FIGURE 40 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 40 Genitalia of S. wolvi sp. nov., AM C.581912, Wolvi Lookout, Mt Salmon. A. Reproductive system. Arrow shows the junction of the penis and epiphallus. B. Penis interior. C. Downloaded Spermatophorefrom. Scale bars Brill. com10/17/20221 mm 12:50:28PM (A–B), 2 mm (C). via free access
FIGURE 39 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 39 Stanisicarion spermatophores (Clade C). A–B. S. aquila, MO77158. C–D. S. aquila, AM C.269856. E–F. S. wolvi, AM C.581912.
FIGURE 38 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 38 Genitalia of S. aquila, MO23337, McDonald NP. A. Reproductive system. Arrow shows the junction of the penis and epiphallus. B. Penis interior. C. Spermatophore. Scale bars 1 mm.
FIGURE 36 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 36 Stanisicarion live images (Clade C). A. Stanisicarion freycineti, Emu heights, Sydney (image J. Wradjan). B. Stanisicarion freycineti, AM C.506245, Oxley Wild Rivers NP. C. Stanisicarion aquila, C.512654, Broken Head. D. Stanisicarion aquila, C.512596, Mt Tamborine. E. Stanisicarion aquila, C.269856, Cicada Glen Creek.
FIGURE 37 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 37 Genitalia of S. freycineti, MO71655, Ingleburn. A. Reproductive system. Arrow shows the junction of the penis and epiphallus. B. Penis interior. Scale bars 2 mm.
FIGURE 35 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 35 Shells of synonyms of Stanisicarion freycineti. A. Vitrina inflata, NHMUK 1977079 (syntypes). B. Vitrina strangei, NHMUK 1983076 (syntypes). C. Vitrina robusta, NHMUK 1926.9.1.63-73 (possible syntypes). All images NHMUK.
FIGURE 34 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 34 Shells of Stanisicarion. A. Stanisicarion freycineti, MO70449. B. Stanisicarion aquila, MO49825. C. Stanisicarion wolvi sp. nov., AM C.581912. Scale bar 5 mm.
FIGURE 31 Genitalia. A–B. F in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 31 Genitalia. A–B. F. rowani, MO85839, Gladstone. C–E. F. sarina, MO85840, Sarina. A, C. Reproductive system. Arrows show the junction of the penis and epiphallus. B, D. Penis interior. E. spermatophore. Scale bars 1 mm (C–E), 2 mm (A–B).
FIGURE 22 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 22 Spermatophores of Clade B species. A-B. F. alyssa, MO77158. C-D. F. deensis, MO85834. E-F. F. hannianus, MO72277. G-H. F. mcdonaldi, MO50434. I-J. F. minerva, MO78358.
FIGURE 30 Genitalia. A-B. F in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 30 Genitalia. A-B. F. papillosus, MO78896, Mt Superbus. C-D. F. pustulosus, MO78894, Mt Fort William. A, D. Reproductive system. Arrows show the junction of the penis and epiphallus. B–C. Penis interior. Scale bars 2 mm.
FIGURE 23 Genitalia. A–C. F in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 23 Genitalia. A–C. F. deensis, MO85834, Mt Morgan. D-E. F. ephelis, MO85835, Broken River. A, D. Reproductive system. Arrows show the junction of the penis and epiphallus. B, E. Penis interior. F. Spermatophore. Scale bars 1 mm (E), 2 mm (A–D).
FIGURE 15 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 15 Genitalia of F. griseolus, MO55568, Bobby Range. A. Reproductive system. Arrow shows the junction of the penis and epiphallus. B. Penis interior. Scale bars 1 mm (B), 2 mm (A).
FIGURE 32 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 32 Genitalia of F. tuljun, MO76081, Denham Range. A. Reproductive system. Arrow shows the junction of the penis and epiphallus. B. Penis interior. Scale bars 1 mm.
FIGURE 18 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 18 Distribution of Clade B species. █ = F. alyssa, ▼ = F. deensis, × = F. ephelis, ♢ = F. hannianus, ▲ = F. insularis, ◻ = F. katatonos, ∆ = F. longimentula, ● = F. mcdonaldi, ♠ = F. minerva, ◆ = F. papillosus, ♣ = F. pustulosus, ♥ = F. rowani, Ǫ = F. sarina, ▽ = F. tuljun.
FIGURE 14 Shell microsculpture. A–C in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 14 Shell microsculpture. A–C. Fastosarion griseolus, MO55568 (A = protoconch, B = early teleoconch, C = late teleoconch). D. Fastosarion alyssa, F230784 (protoconch). E–F. Fastosarion minerva, MO65418 (E = protoconch, F = teleoconch). G–I. Fastosarion papillosus, MO78896 (G = protoconch, H = early teleoconch, I = late teleoconch). J–L. Stanisicarion aquila, MO49825 (J = protoconch, K = early teleoconch, L = late teleoconch). Scale bars 20 µm (A, D, E, I), 100 µm (B, F, L), 50 µm (C, G-H, J-K).
FIGURE 3 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 3 Best maximum likelihood tree based on analysis of the concatenated data set of fragments of the mitochondrial genes 16S and COI using IQ-TREE, with reduced taxon sampling (including only the ingroup). Ambiguous alignment sites in 16S removed using Guidance2. Numbers on branches indicate nodal support based on 10,000 ultra-fast bootstrap repeats as well as by employing Shimodaira-Hasegawa's (1999) approximate Likelihood Ratio Test ('SH-aLRT'). Scale bar indicating 10% of modelled sequence divergence. Shells shown to scale.
FIGURE 2 in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)
FIGURE 2 Majority-rule consensus tree based on Bayesian analysis of the concatenated data set of fragments of the mitochondrial genes 16S and COI. Ambiguous alignment sites in 16S removed using MAFFT. Numbers on branches indicate posterior probabilities. Scale bar indicating 40% of modelled sequence divergence. Shells shown to scale.
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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.