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Figure 5. Bayesian Inference tree calculated with complete cox1 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species
Figure 5. Bayesian Inference tree calculated with complete cox1 (1428 bp), cox3 (753 bp), and cytb (1127 bp) sequences of haemosporidian parasites and Klossiella equi (MH203050) and Klossia razorbacki (MT084562) as the outgroup. Bayesian posterior probabilities and Maximum Likelihood bootstrap values are indicated at most nodes. The scale bar indicates the expected number of substitutions per site according to the model of sequence evolution applied.
Figure 4 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species
Figure 4. Median-Joining DNA haplotype network showing the host and geographic distribution of six Haemoproteus nisi group lineages (478 bp cytb sequences) found in accipitriform raptors from Austria and France.
Figure 3. Phylogenetic tree inferred from cytochrome B in Phlebotomus (Paraphlebotomus) chabaudi and Phlebotomus riouxi: closely related species or synonyms?
Figure 3. Phylogenetic tree inferred from cytochrome B data of Phlebotomus chabaudi and Ph. riouxi specimens. We added to the analysis the sequences of Ph. chabaudi published by Tabbabi et al. (2014). The phylogram results from bootstrapped data sets obtained using the PhyML 3.0 program [21] using GTR (general time reversible) + G distribution (gamma distribution of rates with four rate categories). The tree was visualized using the TreeDyn program, version 198.3 [7]. The percentages above the branches are the frequencies with which a given branch appeared in 500 bootstrap replications. Only bootstrap values higher than 50% on the early branches are shown. A sequence of Ph. sergenti (AF161216) was used as the outgroup. The sequences marked by * were published by Tabbabi et al. (2014); R = sequences found in specimens morphologically characterized as Ph. riouxi. C = sequences found in specimens morphologically characterized as Ph. chabaudi. RC = sequences found in specimens morphologically characterized as Ph. chabaudi or Ph. riouxi. Int = sequences found in specimens morphologically characterized as intermediate between Ph. riouxi and Ph. chabaudi.
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 in A warning for ecologists and conservation biologists using species checklists: How the European marine fauna 'lost' all of its 16 Discodoris species (Mollusca: Gastropoda)
Fig. 2 Phylogenetic tree representing relationships within Discodorididae. The latter contains about 400 species and 40 genera, only some of which are mentioned here, with special emphasis on the genera that contain species originally described in Discodoris. Tree terminal taxa are labeled with the specific epithet followed by the generic name of the original combination in parenthesis. The current generic names are given on the right side of the braces indicating the (few) species per genus mentioned. Assignment of a generic name to a clade is based on a type species that belongs to that clade (e.g., Discodoris boholiensis is the type species of Discodoris). All genera correspond to clades, with the exception of "Montereina", a metaphyletic group at the base of Discodorididae for which no autapomorphic, diagnostic features could be found. For additional information on phylogenetic analyses, authorship of species names, etc., see Dayrat (2010a)
Fig. 3 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)
Fig. 3. Illustration of the morphology of Colpodella, Perkinsus, and Parvilucifera which is indicated to be the plesiomorphic condition for the Alveolata. Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.
Fig. 1 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)
Fig. 1. Consenses of optimal trees found from parsimony analysis of SSU rDNA aligned with MALIGN using all aligned sites (A), only conservative sites (B), and excluding outgroup taxa for all sites (C) and conservative sites only (D). Branches are drawn proportional to amount of change. Values at internodes for groups of interest are parsimony jackknife support indices (asterisk indicates not supported with this method). Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.
Fig. 2 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)
Fig. 2. Consenses of optimal trees found from parsimony analysis of combined 18S rDNA and actin nucleotide sequences (SSU rDNA data were only available for 24 taxa) for all available sites (A) and for conservative SSU rDNA sites (B); values at internodes are Bremer support indices. Optimal tree (C) found for combined analyses using only those taxa for which both genes are available; values at internodes are Bremer support indices for the 18S rDNA data (above nodes) and for the actin data (below nodes). Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.
Fig. 3. Emoleptalea mozambiquensis n in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 3. Emoleptalea mozambiquensis n. sp. from intestine of turquoise killifish, Nothobranchius furzeri Jubb. Dorsal view of ovarian complex. Mehlis' gland cells and eggs are omitted. Abbreviations: anterior testis, at; Laurer's canal, Lc; ovary, ov; oviduct, od; ootype, oo; posterior testis, pt; proximal uterus, pu; seminal receptacle, sr; vitelline follicle, vf; vitelline reservoir, vr.
Fig. 6 in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 6. Ventral view of Heterorchis cf. crumenifer from the intestine of the West African lungfish, Protopterus annectens (Owen). Abbreviations: caecum, c; cirrus, ci; cirrus sac, cs; dorsal opening to excretory bladder, do; distal portion of seminal vesicle, ds; distal uterus, du; excretory bladder, eb; excretory duct, ed; genital atrium, ga; genital pore, gp; left testis, lt; metraterm, m; ootype, oo; ovary, ov; pars prostatica, pp; proximal portion of seminal vesicle, ps; proximal uterus, pu; right testis, rt; seminal receptacle, sr; vitelline follicle, vf; vitelline reservoir, vr.
Fig. 7 in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 7. Dorsal view of excretory system of Heterorchis cf. crumenifer from intestine of the West African lungfish, Protopterus annectens (Owen). Abbreviations: cd; collection ducts, ep; excretory pore, ms; main stem of excretory bladder, ob; oval or elongated bladders, os; oral sucker, vs; ventral sucker.
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b in Unexpected absence of exo-erythrocytic merogony during high gametocytaemia in two species of Haemoproteus (Haemosporida: Haemoproteidae), including description of Haemoproteus angustus n. sp. (lineage hCWT7) and a report of previously unknown residual bodies during in vitro gametogenesis
Fig. 1. Bayesian phylogenetic tree constructed using partial cytochrome b sequences of 61 lineages of Haemoproteus, 4 lineages of Plasmodium, and Leucocytozoon sp. lSISKIN2 as outgroup. Posterior probabilities higher than 0.8 are indicated close to the respective nodes. Red font indicates the parasite lineage described in this publication. Vertical bars (A–D) show groups of closely related lineages, which complete development and produce gametocytes only in non-passerines (A, D), both non-passerines and passerines (B), and only passerines (C). Blue font indicates Haemoproteus species, which develop in non-passerine avian hosts, which are indicated by symbols (● – Psittaciformes; ∎ - Coraciiformes; ▴ - Strigiformes; ◆ - Anseriformes; ★ - Charadriiformes; ♥ - Pelecaniformes; ⋄ - Piciformes; ⊠ - Sphenisciformes; Ω - Musophagiformes; § - Trochiliformes; Ψ – Falconiformes; Σ – Columbiformes; Φ - Galliformes). Lineage names were provided (according to MalAvi database), followed by parasite species names and sequence GenBank accession numbers.
Fig. 8 in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 8. Estimated phylogeny inferred from Bayesian analysis of aligned fragments of the lsrDNA sequences from 40 species of digeneans comprising the ingroup plus one outgroup taxon (Lissorchis kritskyi). Species names are followed by the GenBank accession number for the sequence. New sequences represented by the three studied species are in bold. Posterior probabilities are reported on branches. Scale bar indicates a 5% nucleotide difference.
Fig. 5. Masenia baroensis n in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 5. Masenia baroensis n. sp. from the intestine of the globe fish, Tetraodon lineatus L. Anterior portion from a specimen having the ovary on the right side of the body. Abbreviations: aboral row of circumoral spines, ar; cirrus, ci; cirrus sac, cs; genital atrium, ga; genital pore, gp; metraterm, m; oral row of circumoral spines, or; oral sucker, os.
Fig. 2. Emoleptalea mozambiquensis n in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 2. Emoleptalea mozambiquensis n. sp. from intestine of turquoise killifish, Nothobranchius furzeri Jubb. Dorsal view of anterior end. Note the caeca are surrounded by the vitelline follicles and the terminal genitalia run ventral relative to caeca. This specimen has the ovary on the left side of body. Abbreviations: caecum, c; cirrus, ci; distal portion of seminal vesicle, ds; distal uterus, du; egg, e; genital atrium, ga; genital pore, gp; prostatic bulb, pb; proximal portion of seminal vesicle, ps.
Fig. 4. Masenia baroensis n in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 4. Masenia baroensis n. sp. from the intestine of the globe fish, Tetraodon lineatus L. Ventral view of holotype. Abbreviations: anterior testis, at; caeca, c; cirrus, ci; cirrus sac, cs; excretory bladder, eb; distal portion of seminal vesicle, ds; excretory pore, ep; genital atrium, ga; genital pore, gp; metraterm, m; ovary, ov; pars prostatica, pp; proximal portion of seminal vesicle, ps; posterior testis, pt; uterus (drawn with eggs omitted), u; vitelline follicle, vf.
Fig. 1. Emoleptalea mozambiquensis n in Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids
Fig. 1. Emoleptalea mozambiquensis n. sp. from intestine of turquoise killifish, Nothobranchius furzeri Jubb. Ventral view of holotype. Eggs are omitted from uterus and outline of uterus does not show extensive coiling. Abbreviations: caecum, c; cirrus sac, cs; excretory bladder, eb.
Fig. 3 in Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches
Fig. 3. Proposed life cycle of T. clandestinus and its developmental and morphological features in caiman blood and leeches. Giemsa-stained blood smears showed blood trypomastigotes of experimentally-infected Caiman yacare, and epi- and trypomastigotes found in the gut of one leech of the genus Haementeria sp. collected in the mouth of a wild Cayman yacare captured in the Pantanal wetland of Brazil. The caiman and the leech trypanosomes were molecularly identified as T. clandestinus. (a‾c) epimastigotes; (b) epimastigote dividing by binary fission; (d, g) short trypomastigote; (e,f) long and thin trypomastigotes. Arrow points to the long and thin posterior extremity of very long and slender trypomastigotes. K, kinetoplast; N, nucleus; F, flagellum.
Fig. 2 in Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches
Fig. 2. Phylogenetic tree (ML) based on gGAPDH sequences showing the Terrestrial and Aquatic clades of Trypanosoma and the positioning of T. clandestinus. The Crocodilian clade, which is formed by T. terena, T. ralphi, T. gray and Cay03 nests in the Terrestrial Clade whereas the Clandestinus clade comprising T. clandestinus nests in Aquatic clade. Typanosomatid genera other than Trypanosoma were used as outgroups in the phylogenetic trees (608 characters, Ln = —7611.897017). Numbers at nodes are bootstrap support (P/ML)>50% and Bayesian posterior probability>0.25 derived from 500 replicates.
Fig. 1 in Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches
Fig. 1. Geographical origin of crocodilian trypanosomes included in the V7V8 SSU rRNA dendrogram inferred to compare the barcode sequences between the new and known trypanosomes from crocodilians and other species of aquatic and semi aquatic hosts. The clade comprising T. clandestinus n. sp. nested into the Aquatic clade closely related to fish trypanosomes whereas sequences of the other new species formed the clade Cay03, which clustered with T. terena, T. grayi and T. ralphi in the Crocodilian Terrestrial clade. The host species and geographic origin and Genbank accession numbers of sequences from the crocodilian trypanosomes are shown in Table 1. Numbers at nodes are bootstrap support values>50% (P/ML) derived from 500 replicates.
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 in Three species of Echinococcus granulosus sensu lato infect camels on the Arabian Peninsula
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 reference sequences. The Saudi Arabian haplotypes (H01-09) are in bold. The reference sequences along with their accession numbers and origin of isolate were included for each. T. solium was used as an outgroup taxon. The branch to outgroup was shortened by 0.2 substitutions per site
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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.