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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>
Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria: phylogenetic data
<p>Alignments, trees and Biogeobears analyses related to the study: Leliaert F, Payo DA, Gurgel CFD, Schils T, Draisma SGA, Saunders GW, Kamiya M, Sherwood AR, Lin S-M, Huisman John M, Le Gall L, Anderson RJ, Bolton John J, Mattio L, Zubia M, Spokes T, Vieira C, Payri CE, Coppejans E, D'hondt S, Verbruggen H, De Clerck O. Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography. 2018;45(10):2299-313. doi:10.1111/jbi.13410</p> <p>Abstract: Biogeographical processes underlying Indo-Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals. Species diversity estimates were inferred using DNA-based species delimitation methods. Historical biogeographical patterns were inferred based on a six-gene time-calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographic range evolution. The importance of geographic isolation for speciation was further evaluated by population genetic analyses at the intraspecific level. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo-Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long-term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA. Our results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.</p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the eastern Andean slopes and the biogeographic history of the genus"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the Amazon foothills and the biogeographic history of the genus"</p> <p>The matrix is in NEXUS format and has 3259 bp and 25 terminals.</p> <p>Partitions are as follows:</p> <div>charset 12S = 1-955;</div> <div>charset ND1_nonCoding1 = 956-1279;</div> <div>charset ND1_Pos1 = 1280-2240\3;</div> <div>charset ND1_Pos2 = 1281-2241\3;</div> <div>charset ND1_Pos3 = 1282-2242\3;</div> <div>charset ND1_nonCoding2 = 2243-2361;</div> <div>charset cmyc_Pos1 = 2362-2779\3;</div> <div>charset cmyc_Pos2 = 2363-2780\3;</div> <div>charset cmyc_Pos3 = 2364-2781\3;</div> <div>charset Rag1_Pos1 = 2782-3415\3;</div> <div>charset Rag1_Pos2 = 2783-3416\3;</div> <div>charset Rag1_Pos3 = 2784-3417\3;</div>
Coat protein (CP) and trimmed replication-associated protein (Rep) amino acid alignments, phylogenetic analyses, and associated metadata for ICTV-approved begomovirus RefSeq species exemplars
<p>DATA RETRIEVAL</p> <p>Annotated begomovirus coding sequences corresponding to each begomovirus species exemplar with a RefSeq accession number listed in the ICTV Virus Metadata Resource (VMR #18, 2021-10-19, <a href="https://ictv.global/vmr">https://ictv.global/vmr</a>) were downloaded from GenBank in protein FASTA file format. CP and Rep amino acid sequences were extracted and split into separate data sets for analysis. We confirmed the identity of misannotated ORF products by performing a BLAST search. For exemplar sequences missing ORF annotations (listed in metadata spreadsheet), ORFfinder (<a href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</a>) was used to identify CP and Rep ORFs that were subsequently translated and added to each corresponding data set after BLAST confirmation.</p> <p>ALIGNMENTS</p> <p>Multiple sequence alignments were constructed using the MUSCLE method (Edgar, 2004) as implemented in MEGA 11 (Tamura et al., 2021) and manually corrected using AliView v1.26<strong> </strong>(Larsson, 2014). After an initial alignment inspection, exemplars with either severely truncated (i.e., length < 50% of the average length of the protein) or very divergent (i.e., causing us to doubt protein homology) CP or Rep sequences were excluded from the data set. Due to the difficulties in aligning the Rep sequences at the N- and C- terminal ends, the Rep alignment was trimmed to eliminate all residues prior to the iteron related domain (i.e., the known Rep functional region closest to the Rep start (Arguello-Astorga & Ruiz-Medrano, 2001)) in the N-terminus and after a conserved geminivirus motif found near the C-terminus, which corresponds to where other circular, Rep-encoding single-stranded DNA viruses possess an arginine finger motif (Kazlauskas et al., 2019; Krupovic et al., 2020). In total, our CP and Rep data sets contained amino acid sequences from 432 begomovirus species exemplars that met our inclusion criteria.</p> <p>PHYLOGENETIC ANALYSIS</p> <p>Maximum likelihood (ML) trees were inferred with IQ-Tree v2.0.7 (Minh et al., 2020) using the best fitting substitution model identified by the built-in ModelFinder feature (Kalyaanamoorthy et al., 2017). Tree inference was performed with 3000 ultrafast bootstrap (UFBoot) replicates, a perturbation strength of 0.2 and a stopping rule requiring an iteration interval of 500 iterations between unsuccessful improvements to the local optimum. The -bnni flag was enabled to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The provided phylogenies in NEXUS format are midpoint-rooted and branches are colored based on traditional begomovirus geographic groupings: exemplars sampled in the Americas in orange and exemplars sampled in the 'Africa, Asia, Europe and Oceania' (AAEO) region in blue. </p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species exemplar (n=445) – including country of isolation, geographic designation (i.e., AAEO/Americas), genome segmentation (i.e., monopartite/bipartite), presence/absence of V2/AV2 gene and length of genome/DNA-A segments – are included. Exemplars not incorporated into the other analyses are highlighted in red on the spreadsheet.</p> <p> </p>
Fig. 4 in A new species of Characidium (Characiformes: Crenuchidae) from coastal basins in the Atlantic Rainforest of eastern Brazil, with phylogenetic and phylogeographic insights into the Characidium alipioi species group
Fig. 4. Fast flowing stream, type locality of Characidium cricarense, at Cachoeira do Inferno rapids in rio Cricaré, São Mateus, ES, Brazil. GPS coordinates: 18°42'24.5"S 40°16'7.2"W.
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication in Rediscovery of Andrea's keelback, Hebius andreae (Ziegler & Le, 2006): First country record for Laos and phylogenetic placement
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication
Fig. 5 in Description of a new species of Moenkhausia (Characiformes: Characidae) from the upper Paraguay basin, Central Brazil, with comments on its phylogenetic relationships
Fig. 5. Map showing the localities of Moenkhausia flava. Red star represents the type locality. Black square represents the Salto das Nuvens fall and the white square represents Salto Maciel fall.
Figure 8. E in Phylogenetic analysis of species of the neotropical social wasp Epipona Latreille, 1802 (Hymenoptera, Vespidae, Polistinae, Epiponini)
Figure 8. E. niger, propodeum, dorsal view. Scale bar = 1.0 mm. Figure 9. E. guerini, propodeum, dorsal view. Scale bar = 1.0 mm. Figure 10. E. niger, head, dorsal view. Scale bar = 1.0 mm. Figure 11. E. guerini, head, dorsal view. Scale bar = 1.0 mm. Figure 12. E. tatua, Tergum II, dorsal view. Scale bar = 1.0 mm. Figure 13. E. media, Tergum II, dorsal view. Scale bar = 1.0 mm.
Figure 1. E in Phylogenetic analysis of species of the neotropical social wasp Epipona Latreille, 1802 (Hymenoptera, Vespidae, Polistinae, Epiponini)
Figure 1. E. quadrituberculata, humeri, dorsal view. Scale bar = 1.0 mm. Figure 2. E. tatua, humeri, dorsal view. Scale bar = 1.0 mm. Figure 3. E. guerini, propodeal concavity, frontal view. Scale bar = 1.0 mm. Figure 4. E. tatua, propodeal cancavity, frontal view. Scale bar = 1.0 mm. Figure 5. E. quadrituberculata, Tergum I, dorsal view. Scale bar = 1.0 mm. Figure 6. E. tatua, Tergum I, dorsal view. Scale bar = 1.0 mm.
Figure 13 in Phylogenetic analysis of species of the neotropical social wasp Epipona Latreille, 1802 (Hymenoptera, Vespidae, Polistinae, Epiponini)
Figure 13. Cladogram of species of Epipona. Character numbers (see table 1) are placed above hash marks, with the state numbers below, separated by ">" to indi- cate the transitions between states. Filled hash marks indicate an uncontroverted step, while open hash marks indicate homoplastic change.
Fig. 3. Phylogenetic relationships among a in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)
Fig. 3. Phylogenetic relationships among a curated set of COI barcode sequences for Rasopone. Black samples were sequenced for UCEs. Red samples were downloaded from the BOLD database.The tree was inferred using IQ-TREE with the data partitioned by codon position. Black circles on nodes indicate high support, which we define as ≥95% ultrafast bootstrap support and ≥95% SH-like branch support.Terminal names match taxonomic changes proposed in paper and provide useful sample identifiers (e.g., extraction codes [EX#] or BOLD process IDs).A complete, unpruned COI tree is available in Supp Fig. S1 (online only).
Fig. 4 in A new genus and species of uncertain phylogenetic position within the family Hydrobiidae (Caenogastropoda, Truncatelloidea) discovered in Tunisian springs
Fig. 4. Radula of Bullaregia tunisiensis gen. et sp. nov. from a spring in Djebba, Tunisia. A. Rows of teeth of the radula. B. Detail of central teeth. C. Detail of lateral and marginal teeth.
Fig. 2 in A new genus and species of uncertain phylogenetic position within the family Hydrobiidae (Caenogastropoda, Truncatelloidea) discovered in Tunisian springs
Fig. 2. Maximum likelihood inference based on COI dataset. Bootstrap values and BPP's are given when ≥ 70% and 0.90, respectively. Black bars on the right indicate subfamily assignments. Scale bar: expected change per site.
Fig. 3 in A new genus and species of uncertain phylogenetic position within the family Hydrobiidae (Caenogastropoda, Truncatelloidea) discovered in Tunisian springs
Fig. 3. Bullaregia tunisiensis gen. et sp. nov. A. Shell (holotype). B. Operculum. C. Head and penis. D. Coiled body.
Fig. 5 in A new genus and species of uncertain phylogenetic position within the family Hydrobiidae (Caenogastropoda, Truncatelloidea) discovered in Tunisian springs
Fig. 5. Genitalia of Bullaregia tunisiensis gen. et sp. nov. A. Penis (paratype). B. Distal female genitalia. Abbreviations: bc = bursa copulatrix; ov = renal oviduct; SR = seminal receptacle. Scale bar 0.1 mm.
Fig. 6 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 6. Paratypes of Pristimantis boucephalus sp. nov. in dorsal (upper row) and ventral (lower row) views. From left to right: ♀ (MUSM 24479), ♂ (MUSM 24477), ♂ (MUSM 24478), juvenile (MUSM 24474). Photos by E. Lehr.
Fig. 7 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 7. Type locality of Pristimantis boucephalus sp. nov. in the Yanachaga-Chemillén National Park. Photo by E. Lehr.
Fig. 4 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 4. Preserved holotype (MUSM 31102, SVL 14.1 mm) of Pristimantis boucephalus sp. nov. A. Dorsal view. B. Ventral view. Photos by E. Lehr.
Fig. 5 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 5. Pristimantis boucephalus sp. nov., holotype (MUSM 31102). A. Dorsal view of head. B. Lateral view of head. C. Ventral view of hand. D. Ventral view of foot. Drawings by J. Moravec.
Fig. 3 in A new minute species of Pristimantis (Amphibia: Anura: Craugastoridae) with a large head from the Yanachaga-Chemillén National Park in central Peru, with comments on the phylogenetic diversity of Pristimantis occurring in the Cordillera Yanachaga
Fig. 3. Live holotype (MUSM 31102, SVL 14.1 mm) of Pristimantis boucephalus sp. nov. A. Dorsal view. B. Dorsolateral view. C. Ventral view. Photos by E. Lehr.
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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.