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Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D in Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA
Figure 2. Bayesian phylogram for cytochrome c oxidase subunit I sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D. Posterior probability values ≥ 90% are shown. Upper Sacramento River basin lineages newly discovered in this study are highlighted by the larger font. Specimen codes are from Table 1.
Fig. 1 in Populations analysis of the Brazilian Sharpnose Shark Rhizoprionodon lalandii (Chondrichthyes: Carcharhinidae) on the São Paulo coast, Southern Brazil: inferences from mt DNA sequences
Fig. 1. Median-joining haplotype network. The haplotypes are represented by circles, with the width proportional to their frequencies. Black circles correspond to Praia Grande, white to Ubatuba, and gray to Itanhaém samples. Each branch corresponds to a single mutation, except line a (with 2 mutations) and line b (with 3 mutations).
Figure 1 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 1. Morphology and infraciliature of Psammomitra retractilis (F–J, from Song & Warren, 1996). A, B, F, individuals in extended states to show the typical body shapes. Arrowheads in (A) mark the long, dominant membranelles. C, lateral view of a contracted specimen. D, posterior part, to demonstrate the long dorsal cilia. E, anterior part. Arrowheads indicate the long membranelles, whereas arrows mark the dorsal cilia. G, H, dorsal and lateral views of contracted cells. I, J, ventral and dorsal views to show the infraciliature and macronuclear nodules. Scale bars: A, C, D, F = 40 Mm; E = 30 Mm.
Figure 3 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 3. Maximum parsimony phylogeny of small subunit rRNA genes. Psammomitra is highlighted in black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. Numbers on branches are values generated from 1000 bootstrap replicates.
Figure 2 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 2. Phylogenetic tree based on small subunit rRNA sequences showing the position of Psammomitra retractilis, by Bayesian inferences applying the GTR + G + I model. '-' reflects disagreement between a method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Psammomitra is shaded black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. The scale bar corresponds to five substitutions per 100 nucleotide positions. Infraciliature of Oxytricha and Uroleptus (from Foissner et al., 2004), Amphisiella (from Li et al., 2007), Trachelostyla (from Gong et al., 2006), and Holosticha (from Hu & Song, 2001) are also shown.
Figure 4 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 4. Bayesian trees based on different data sets showing phylogenetic relationships amongst Spirotrichea. '-' reflects disagreement between the maximum likelihood/ maximum parsimony method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Species sequenced in the present study are shown in bold type. The scale bar corresponds to 10/2 substitutions per 100 nucleotide positions. A, phylogenetic analyses inferred from alpha-tubulin gene sequences data set. B, phylogenetic analyses inferred from alpha-tubulin amino acids data set.
Figure 4 in Comparative ossification sequence and skeletal development of the postcranium of palaeognathous birds (Aves: Palaeognathae)
Figure 4. Graph of stage (Hamburger & Hamilton, 1951) of first occurrence of ossification for fore- and hindlimb elements for chicken, turkey, emu and rhea embryos. The order in which the elements are presented is standardized against the chicken sequence. Stage 40.5 is the same as stage 40+ in the text, whereas stage 45 represents elements that are ossified in the adult but unossified in the oldest embryo examined. The digit number is in roman numerals; the phalanges are numbered proximally to distally in arabic numerals.
Figure 2 in Comparative ossification sequence and skeletal development of the postcranium of palaeognathous birds (Aves: Palaeognathae)
Figure 2. Lateral view of the hindlimb and pelvic girdle of palaeognath embryos. A–C, Dromaius novaehollandiae: A, stage 32 (RM 8052); B, stage 36 (day 25 of incubation, RM 8023); C, stage 40+ (day 36 of incubation, RM 8034). E–G, Struthio camelus: E, day 15 of incubation (YPM 112437); F, day 21 of incubation (YPM 112444); G, day 34 of incubation (YPM 112459). I, J, Eudromia elegans: I, day 10 of incubation (YPM 112520); J, day 15 of incubation (YPM 112525). D, H, Rhea americana: D, stage 34 (day 14 of incubation, RM 7217); H, stage 40+ (day 26 of incubation, RM 7223). Grey shaded regions represent cartilage; black regions represent ossified tissue. The density of stippling reflects the relative degree of ossification. Scale bar, 5 mm.
Figure 3 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 3. Phoronid phylogeny. Most probable Bayesian likelihood tree (P = 0.68) from analysis of the 13tx alignment with clade credibility values from the majority rule consensus tree, which had the same topology. Where two clade credibility values are shown the first was from a run with the chiton as outgroup (not shown), and the second from a run with Phoronis ovalis as outgroup. MrBayes run commands were: charset coding_1st = 1-621\3; charset coding_2nd = 2-621\3; charset coding_3rd = 3-621\3; charset non-coding = 622-4515; partition all_4 = 4: coding_1st, coding_2nd, coding_3rd, non-coding; set partition = all_4; lset applyto=(all) nst = 6 rates = invgamma; databreaks 621 2386; unlink shape = all, pinvar = all, statefreq = all, revmat = all; prset ratepr = variable; mcmc ngen = 106 samplefreq = 100 printfreq = 5000 savebrlens = yes; plot match = all; sumt burnin = 2002. The tree shown was drawn in PAUP*4. The.con file was imported and displayed as a phylogram. Clade credibility values were added in a graphics editor.
Figure 2 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 2. Phoronid phylogeny. Maximum likelihood phylogram based on 24tx alignment of concatenated rDNA sequences, with selected bootstrap values (%, 100 pseudoreplicates).
Figure 1 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 1. Phoronid phylogeny. Reweighted parsimony cladogram (length = 36.75, consistency index = 0.907, retention index = 0.899) based on a 24-character morphological data matrix with bootstrap support (%; 500 pseudoreplicates; first figure unweighted, second figure reweighted).
Figure 3 in Comparative ossification sequence and skeletal development of the postcranium of palaeognathous birds (Aves: Palaeognathae)
Figure 3. Comparable developmental stages of Meleagris gallopavo (A), Rhea americana (B) and Dromaius novaehollandiae (C). Each embryo is at stage 34 (Hamburger & Hamilton, 1951) and to the same scale. Arrows mark the proximal and distal extents of the developing wings. Scale bar, 1 cm.
Figure 2. Phylogenetic relationships among the 29 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 2. Phylogenetic relationships among the 29 specimens of Orthometopon species. Individuals from two other terrestrial isopod species were used as outgroup taxa: Ligidium sp. and Armadillidium vulgare. Phylogenetic analyses, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), all produced trees with the same topology. Only the BI tree is presented here. Numbers above the branches indicate bootstrap values in the MP and ML analyses, respectively (MP/ML). Numbers below the branches indicate the posterior probabilities of the Bayesian analysis (BI).
Figure 1 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 1. Map showing the sampling localities of the 29 specimens used for the DNA analysis. The numbers correspond to those listed in Table 1.
Figure 5 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 5. Summary cladogram representing the relationships of the anomalodesmatan family-level taxa inferred from the 18S rRNA data. Asterisks indicate lacking support for the monophyly of the taxon.
Figure 3 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 3. Maximum-likelihood tree under an HKY85+I+G model (–logL = 25513.945, s/v ratio = 1382, pinvar = 0.189, gamma = 0.463).
Figure 2 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 2. Strict consensus tree of 22 most parsimonious trees using all alignment positions of the 18S rRNA data set. Bootstrap values (above branches) refer to 1000 replications, maximum-likelihood puzzling values (below branches; values lower than 30 not given) refer to 100 000 puzzling steps. A, subtree showing the position of Anomalodesmata among the Heterodonta. B, subtree of the Anomalodesmata. Pha., Pharidae; Ven., Veneridae. Asterisks mark species of the polyphyletic Myoida. Arrowheads indicate the anomalodesmatan nodes collapsing when 506 positions of uncertain alignment in the
Figure 1 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 1. Single most parsimonious tree resulting from the analysis of the entire morphological data set of Harper et al. (2000). Asterisks mark taxa not available for the present study. The Euciroidae as recognized by Poutiers & Bernard (1995) was not separated from the Verticordiidae.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
Figure 3 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 3. The single most-parsimonious tree (L = 951; CI = 0.568; RI = 0.793) obtained from the maximum parsimony analysis of combined (16S + ITS1) sequence dataset. Maximum likelihood analysis produced a largely congruent topology (HKY model; Ln likelihood = - 7034.61154) with the only difference being Pisidium dubium sister to Sphaerium/Musculium clade. Taxonomic names are arranged according to suggested sphaeriinid taxonomy in the present study and five major monophyletic lineages are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups. MP bootstrap values are shown to the left of the slash and decay index values to the right above the branches. Numbers below the branches indicate ML bootstrap values.
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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.