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Fig. 2 in Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)
Fig. 2 Subtree of Phylliroe and its closest relatives from Dendronotida s.s., Dendronotidae, Scyllaeidae, and Tethyidae. Images from life animals and histological slides. a Dendronotus venustus. b, c Dendronotus frondosus. d–f Crosslandia viridis. g–i Melibe leonina. j–l Phylliroe
Fig. 1 in Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)
Fig. 1 Maximum likelihood phylogeny of Cladobranchia from RAxML-NG using a concatenat- ed nucleotide matrix of 292 genes partitioned by codon position. All nodes with no support values in- dicated have 100% bootstrap support and a posterior probability of 1.0 in our analyses. The blue box indicates Dendronotida sensu stricto and the red outline shows the closest relatives to Phylliroe in our analysis (Melibe leonina, Tethyidae; Scyllaea fulva, Scyllaeidae; Dendronotus venustus, Dendronotidae), highlighted further in Fig. 2
Supplementary material 1 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Data Table. Taxon sample and UCE sequencing results : Explanation note: Samples highlighted in red were sequenced for Starrett et al. (2017).
Fig. 2 in Application of genomic markers generated for ray-finned fishes in chondrichthyan Phylogenomics
Fig. 2 Phylogenomic relationship of investigated 26 jawed fish species based on single-copy orthologous exon markers. Bootstrap values are shown in each node
Fig. 1 in Application of genomic markers generated for ray-finned fishes in chondrichthyan Phylogenomics
Fig. 1 Phylogenomic relationships of investigated chondrichthyans based on two approaches in this study. Branches with inconsistency in phylogenomic inferences between BUSCO and exon approaches were denoted with red stars. Colors highlighted orders of Chondrichthyes
Fig. 2 in A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata)
Fig. 2 Left. Bayesian inference of the phylogenetic tree based on the concatenated sequences of the nuclear marker 28S rRNA and the mitochondrial 16S rRNA, NADH dehydrogenase (ND1), 12S rRNA, and COI. Right. Phylogenetic tree based on the same analysis but imple-
Fig. 1 in Phylogenomic analysis with improved taxon sampling corroborates an Alydidae + Hydarinae + Pseudophloeinae clade (Heteroptera: Coreoidea: Alydidae, Coreidae)
Fig. 1 Summary of phylogenetic hypotheses based on previous morphological and molecular cladistic analyses
Fig. 1 in Finding a home for the ram's horn squid: phylogenomic analyses support Spirula spirula (Cephalopoda: Decapodiformes) as a close relative of Oegopsida
Fig. 1 IQ-TREE maximum likelihood phylogram recovered in partitioned analysis of the 50% filtered OrthoFinder data matrix incorporating the decapodiform substitution model. Spirula spirula and major cephalopod clades are highlighted in bold. Numbers near the branches are gene concordance factors/site concordance factors. ML bootstrap
FIGURE 3 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 3. Phylogenetic tree of Vitis based on large single copy region inferred from maximum likelihood (ML) analysis based on IQTREE website. Purple branches represent species from North America, yellow branch represent species from Europe, and green branches represent species from Asia. Value of ultrafast bootstrap approximation are indicated on the branches.
FIGURE 2 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 2. Sliding window analysis of the complete chloroplast genome of 13 Vitis taxa (window length: 600 bp, step size: 50 bp). X- axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.
Figure 3. Phylogenomic tree estimated from a in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 3. Phylogenomic tree estimated from a concatenated dataset of 1680 orthogroups of 28 litostomateans and two spirotricheans
Figure 3. Phylogenomic tree estimated from a in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 3. Phylogenomic tree estimated from a concatenated dataset of 1680 orthogroups of 28 litostomateans and two spirotricheans by maximum likelihood (ML) and Bayesian inference (BI) methods. Sequences from the present study are in bold. Ŋe numbers at the nodes are the bootstrap values of ML out of 1000 pseudoreplicates and the posterior probability of Bayesian analysis* respectively. Ŋe black dots represent full support values both in the ML and in the BI trees. º* subclass ºrichostomatia; H* subclass Haptoria; R* subclass Rhynchostomatia.
Figure 4 in Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
Figure 4. Morphological features of Cenophenginae. Cenophengus debilis LeConte, 1881: A, habitus, dorsal; C, head and prosternum, ventral. Cenophengus marmoratus Wittmer, 1976: B, habitus, dorsal; D, aedeagus, dorsal; E, aedeagus, lateral. Scales bars: 2 mm in A, B; 0.5 mm in C; 1 mm in D, E. Tentorial pits are marked with blue arrows, gular sutures with red arrows.
Figure 2 in Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
Figure 2. Overview of Phengodidae phylogenies. A, Zaragoza-Caballero and Zurita-García (2015), morphological characters. B, Quintino (2017), morphological characters. C, Kundrata et al. (2019), four molecular markers. D, Roza (2022), morphological characters.
Figure 3. A in Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
Figure 3. A, four-cluster likelihood mapping test of alternative phylogenetic hypotheses showing the placement of Cenophengus in relationship to other Phengodidae subfamilies. B, phylogeny of Phengodidae inferred from the partitioned maximum-likelihood analysis of the 45% completeness nucleotide matrix (45CPP-NT), based on 358 loci and 35 112 bp. Node circles correspond to selected individual analyses, as identified in the circle key on the left side of the figure. Abbreviations: 45CPP-NT-BI, Bayesian analysis of the partitioned 45% completeness nucleotide matrix; 45CPP-NT-ML, maximum likelihood analysis of the partitioned 45% completeness nucleotide matrix; 45CPU- NT-BI, Bayesian analysis of the unpartitioned 45% completeness nucleotide matrix; 45CPU-NT-ML, maximum likelihood analysis of the unpartitioned 45% completeness nucleotide matrix; PP, Bayesian posterior probabilities of the clades of the majority-rule consensus tree of the posterior distribution generated via the Markov chain Monte Carlo; SH-aLRT, Shimodaira–Hasegawa-like approximate likelihood ratio test; UFBoot, 'ultrafast' bootstrap. Habitus images represent the sampled species; numbers of the images correspond to numbers near tip labels (taxon names); images 1–25 by authors, 26 by Alexander S. Prosvirov, 27 by Amir Weinstein.
Figure 1 in Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
Figure 1. Diversity of Phengodidae. A, Zarhipis integripennis (LeConte, 1874), adult male, USA (credit: Karlyn Lewis, Flickr). B, larva of Phengodes sp. feeding on a millipede [Euryuridae: Euryurus carolinensis (Saussure, 1859)], USA (credit: Matt Bertone, Flickr). C, undescribed Mastinocerinae, adult male, Ecuador (credit: Jim McClarin, Flickr). D, Cydistus reiteri Bourgeois, 1885, adult male, Israel (credit: Ben Theodore, iNaturalist). E, glowing larva or adult female of Mastinocerinae, Ecuador (credit: Jim McClarin, Flickr). F, Cenophengus pallidus
Figure 6 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 6. Phylogeny of Acestrorhamphidae and subfamilies Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, and Hyphessobryconinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.
Figure 4 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 4. Phylogeny of Characidae and subfamilies Aphyocharacinae, Cheirodontinae, Exodontinae, Tetragonopterinae, and Characinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.
Figure 3 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 3. Phylogeny of Spintherobolidae and Stevardiidae and subfamilies Landoninae, Xenurobryconinae, Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, and Diapominae based on 1348 nuclear loci of ultraconserved elements
Figure 2 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 2. Phylogenetic relationships of the major clades of Spintherobolidae, Stevardiidae, Characidae, and Acestrorhamphidae based on the 75% complete matrix of 1348 ultraconserved elements (575 taxa; 538 472 bp).
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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.