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Datasets for phylogenetic analyses and phylogenetic trees for: Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae). Invertebrate Systematics, 2024
<p>We combined the COI sequence data with legacy multigene sequence data to create a new, taxon-rich phylogeny for the Amaurobioidinae. We used sequences for four loci that have been used in previous studies on the subfamily: two mitochondrial loci, COI (658bp) and ribosomal subunit 16S (16S, 410bp); and two nuclear loci, Histone H3 (H3, 327bp) and ribosomal subunit 28S (28S, 839bp). We complemented the Amaurobioidinae data with sequences from several non-amaurobioidine anyphaenids and two clubionids as outgroups. Sequence alignment was performed using the MAFFT (ver. 7.308) plugin in Geneious, allowing MAFFT to automatically select an appropriate alignment strategy based on the properties of each locus, or with the online MAFFT server (https://mafft.cbrc.jp), which consistently selected the L-INS-i algorithm. Finally, alignments of the four loci were concatenated to construct a 2234 bp multigene sequence matrix containing 692 taxa, with about 55% missing/gap data (“full” matrix henceforth). To ensure that excessive missing data did not affect the resulting topology, we also constructed a reduced matrix by removing additional COI-only specimens so that each species and morphotype was represented by just one or two specimens for which all loci were available (where possible). After realignment, this reduced matrix was 2235 bp long, included 167 taxa, and had about 22% missing/gap data (“reduced” matrix henceforth). Phylogenetic analyses under maximum likelihood, including model selection, were then conducted with IQ-TREE 2. We performed phylogenetic analyses on both concatenated matrices (the full matrix and the reduced matrix) and on each individual locus. For model selection, we provided an initial scheme that partitioned the matrix by locus, and further partitioned the protein-coding loci (COI and H3) by codon position. We used ModelFinder and searched for the best partition scheme, all in IQ-TREE. The best models (partitions) for the full dataset were: GTR+F+I+G4 (16S), GTR+F+I+I+R4 (28S), TVM+F+I+I+R2 (COI-1), TIM2+F+R4 (COI-2), GTR+F+R5 (COI-3), TVMe+G4 (H3-1-H3-2), SYM+G4 (H3-3); and for the reduced dataset: GTR+F+I+G4 (16S), GTR+F+I+G4: (28S), GTR+F+I+G4: (COI-2), GTR+F+I+G4: (COI-3), TVM+F+I+G4: (COI-1, H3-2), GTR+F+I+G4: (H3-1), GTR+F+I+G4: (H3-3). For each dataset, once the best models and partitions were defined, we executed 10 independent replicates of tree calculations followed by 1000 ultrafast bootstrap replicates, and the replicate reaching the maximum likelihood was chosen. Phylogenetic analyses under parsimony were made with TNT, under equal weights, using the “new technology” search with default values, asking for 10 independent hits to the minimal length, and submitting the resulting trees to a round of TBR branch swapping. </p>
Fig. 5 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 5. Phylogeny and distribution of the Crematogaster borneensis-group, C. khmerensisi sp. nov., C. fruhstorferi, C. ssAUS5, C. mjobergi and the C. tetracantha-group. Closed circle indicates C. khmerensis sp. nov., closed square indicates C. pfeifferi sp. nov. It is noted that C. pfeifferi sp. nov. is not represented in the phylogeny.
Fig. 4. A–D in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 4. A–D. Crematogaster khmerensis sp. nov., worker. A. Body in lateral view. B. Full-face view of head. C. Dorsal view of mesosoma. D. Petiole and postpetiole in dorsal view. — E–H. — Crematogaster pfeifferi sp. nov., worker. E. Body in lateral view. F. Full-face view of head. G. Dorsal view of mesosoma. H. Petiole and postpetiole in dorsal view.
Fig. 3 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 3. Posterior estimates of divergence time of 24 taxa on the phylogenetic tree. Blue bars depict the 95% highest posterior density (HPD). Estimations were performed with MCMCTree using the independent rate model.
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Above node numbers indicate posterior probability. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %. Area enclosed by dashed lines is enlarged on Fig. 2.
FIGURES 68 73 in Systematic revision of Anopinella Powell (Lepidoptera: Tortricidae: Euliini) and phylogenetic analysis of the Apolychrosis group of genera
FIGURES 68 73. Adults of Anopinella. 68, A. mariana; 69, A. carabayana; 70, A. cafrosana; 71, A. porrasa; 72, A. styraxivora, 73, A. fana.
Figure 51 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 51. Arbitrarily selected tree to trace the character evolution within the cryptobran dorids. Numbers refer to characters listed in the text. Characters printed in bold and italic face presented at least one instance of reversal.
Figure 50 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 50. Majority rule (50%) consensus tree of the phylogenetic relationships of the cryptobranch dorids with the percentage level of consensus.
Figure 48 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 48. Morphology of the caecum. A, Doris verrucosa (CASIZ 082119); scale bar = 1 mm. B, Calycidoris guntheri (CASIZ 086915); scale bar = 1 mm.
Figure 49 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 49. Strict consensus tree of the phylogenetic relationships of the cryptobranch dorids with the Bremer support values in terms of steps.
Figure 47 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 47. SEM images of dorsal tubercles. A, Onchidoris bilamellata (CASIZ 070511); scale bar = 430 Mm. B, Actinocyclus verrucosus (CASIZ 099250), scale bar = 600 Mm. C, Discodoris boholiensis (CASIZ 083654); scale bar = 150 Mm. D, Diaulula sandiegensis (CASIZ 068277); scale bar = 250 Mm.
Figure 46 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 46. Conualevia marcusi (CASIZ 071531). A, general view of the anatomy; scale bar = 1 mm. B, reproductive system; scale bar = 1 mm. C, lateral view of the buccal bulb; scale bar = 0.5 mm. D, central nervous system; scale bar = 0.5 mm. E, ventral view of the mouth area; scale bar = 1 mm.
Figure 45 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 45. Conualevia marcusi (CASIZ 071531), SEM images of a rhinophore and the penis. A, rhinophore; scale bar = 150 Mm. B, penis; scale bar = 150 Mm.
Figure 43 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 43. Sebadoris nubilosa (CASIZ 071727). A, general view of the anatomy; scale bar = 1 mm. B, reproductive system; scale bar = 1 mm. C, detail of several reproductive organs; scale bar = 1 mm. D, central nervous system; scale bar = 1 mm. E, lateral view of the buccal bulb; scale bar = 1 mm. F, ventral view of the mouth area; scale bar = 1 mm.
Figure 44 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 44. Conualevia marcusi (CASIZ 071531), SEM images of the radula and dorsal tubercles. A, inner lateral teeth; scale bar = 15 Mm. B, mid-lateral teeth; scale bar = 25 Mm. C, outer lateral teeth; scale bar = 20 Mm. D, dorsal tubercles; scale bar = 150 Mm.
Figure 42 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 42. Sebadoris nubilosa (CASIZ 071727), SEM images of the radula, penis and dorsal papillae. A, inner lateral teeth; scale bar = 50 Mm. B, mid-lateral teeth; scale bar = 75 Mm. C, outer lateral teeth; scale bar = 43 Mm. D, penial lamellae; scale bar = 100 Mm. E, dorsal papillae; scale bar = 500 Mm.
Figure 41 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 41. Otinodoris sp. (CASIZ 073238), SEM images of the penial hooks and vagina. A, penial hooks; scale bar = 500 Mm. B, vaginal cuticular lining; scale bar = 100 Mm.
Figure 39 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 39. Otinodoris sp. (CASIZ 073238), SEM images of the radula and dorsal tubercles. A, inner lateral teeth; scale bar = 75 Mm. B, mid-lateral teeth; scale bar = 75 Mm. C, outer lateral teeth; scale bar = 43 Mm. D, dorsal tubercles; scale bar = 350 Mm.
Figure 37 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 37. Geitodoris planata (YPM 10405), SEM images of the radula, jaws and dorsal tubercles. A, inner lateral teeth; scale bar = 100 Mm. B, mid-lateral teeth; scale bar = 100 Mm. C, outer lateral teeth; scale bar = 75 Mm. D, jaw elements; scale bar = 30 Mm. E, dorsal tubercles; scale bar = 300 Mm.
Figure 38 in A phylogenetic analysis and systematic revision of the cryptobranch dorids (Mollusca, Nudibranchia, Anthobranchia)
Figure 38. Geitodoris planata (YPM 10405). A, general view of the anatomy; scale bar = 1 mm. B, reproductive system; scale bar = 0.5 mm. C, detail of several reproductive organs; scale bar = 0.5 mm. D, lateral view of the buccal bulb; scale bar = 1 mm. E, ventral view of the mouth area; scale bar = 1 mm. F, central nervous system; scale bar = 1 mm.
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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.