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Figure 7 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 7 Morphology of R clade with corresponding 399_70 UCE RAxML phylogeny (not all bootstrap values shown). Holotype female spermathecal images from Paquin and Dupérré (2009), used with permission. Images not to scale.
Figure 4 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 4 Morphology of ME clade with corresponding 399_70 UCE RAxML phylogeny (not all bootstrap values shown). Holotype female spermathecal images from Paquin and Dupérré (2009), used with permission. Images not to scale.
Figure 3 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 3 Phylogenetic tree from RAxML analysis of COI mitochondrial data. Previously published sequences with corresponding GenBank numbers (AY#), some with cave location codes as in Paquin and Hedin (2004). Bootstrap values above 70 shown only for major lineages. Bootstrap values within C. madla shown on Figure 6, those for C. loftini shown on Figure 10.
Figure 11 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 11 Anomalous geographic distribution of C. venii and C. vespera type specimens. All views ventral.
Figure 10 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 10 Distribution of C. loftini in Culebra Anticline KFR, with corresponding COI RAxML phylogeny. Different mtDNA microclades designated by different colors. Cave locations approximate.
Figure 2 from: Hedin M, Derkarabetian S, Blair J, Paquin P (2018) Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys 769: 49-76. https://doi.org/10.3897/zookeys.769.25814
Figure 2 Phylogenetic tree from BEAST analysis of 399_70 UCE matrix. Posterior probability values above 0.95 shown. Inset: Boxplots of TI values (from Suppl. material 6) for ME and R clade members from Bexar County (for ME clade, two small juveniles and Stahl Cave specimens not included).
FIGURE 4 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 4. Leaves and seeds of Vitis amurensis (A–B) and V. baihuashanensis (C–D).
FIGURE 1 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 1. Gene map of the four Vitis chloroplast genomes.
Table 3 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy
<p>Table 3. Alignment Information.</p><table><tbody><tr><th>Item</th><th>Number of variable sites</th><th>Number of parsimony-informative sites</th><th>Number of constant sites</th><th>Total length (bp)</th></tr></tbody><tbody><tr><th>Phylogenomic alignment</th><td>30 038</td><td>16 845</td><td>76 847</td><td>106 885</td></tr><tr><th>Supermatrix alignment</th><td>30 057</td><td>16 895</td><td>76 657</td><td>106 714</td></tr></tbody></table>
Table 2 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy
<p>Table 2. Taxonomic coverage of sampling from the <i>Eriostemon</i> group.</p><table><tbody><tr><th>Genus</th><th>Section</th><th>Number of species sampled (full plastome data)</th><th>Number of species sampled (Sanger data)</th><th>Total number of species</th></tr></tbody><tbody><tr><th><i>Asterolasia</i></th><td></td><td>2</td><td></td><td>19</td></tr><tr><th><i>Chorilaena</i></th><td></td><td>3</td><td></td><td>4</td></tr><tr><th><i>Correa</i></th><td></td><td>3</td><td></td><td>11</td></tr><tr><th><i>Crowea</i></th><td></td><td>3</td><td></td><td>3</td></tr><tr><th><i>Diplolaena</i></th><td></td><td>2</td><td></td><td>15</td></tr><tr><th><i>Drummondita</i></th><td></td><td>3</td><td>(1)</td><td>11</td></tr><tr><th><i>Eriostemon</i></th><td></td><td>2</td><td></td><td>2</td></tr><tr><th><i>Geleznowia</i></th><td></td><td>1</td><td>(1)</td><td>2</td></tr><tr><th><i>Halfordia</i></th><td></td><td>1</td><td></td><td>1–3</td></tr><tr><th><i>Leionema</i></th><td></td><td>4</td><td></td><td>28</td></tr><tr><th><i>Muiriantha</i></th><td></td><td>1</td><td></td><td>1</td></tr><tr><th><i>Myrtopsis</i></th><td></td><td>1</td><td></td><td>~9</td></tr><tr><th><i>Nematolepis</i></th><td></td><td>3</td><td></td><td>7</td></tr><tr><th><i>Neoschmidia</i></th><td></td><td>1</td><td></td><td>2</td></tr><tr><th><i>Phebalium</i></th><td></td><td>7</td><td></td><td>38</td></tr><tr><th><i>Philotheca</i></th><td><i>Corynonema</i></td><td>3</td><td></td><td>3</td></tr><tr><th></th><td><i>Cyanochlamys</i></td><td>2</td><td></td><td>2</td></tr><tr><th></th><td><i>Erionema</i></td><td>2</td><td>2</td><td>15</td></tr><tr><th></th><td><i>Philotheca</i></td><td>4</td><td>20 (2)</td><td>34</td></tr><tr><th>Total</th><td></td><td>48</td><td>22 (4)</td><td>~206–209</td></tr></tbody></table><p>Numbers in parentheses indicate where the same species was sampled in both the full plastome and Sanger datasets. Total number of species includes described taxa only (i.e. phrase-named species are excluded).</p>
Fig. 4 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy
Fig. 4. (Caption on next page)
Fig. 3 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy
Fig. 3. (Caption on next page)
Linked collectors and determiners for: An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar.
Natural history specimen data linked to collectors and determiners held within, "An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8af27bde-abaa-4f0a-8f84-8b6cc8a97034">https://bionomia.net/dataset/8af27bde-abaa-4f0a-8f84-8b6cc8a97034</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8af27bde-abaa-4f0a-8f84-8b6cc8a97034">https://gbif.org/dataset/8af27bde-abaa-4f0a-8f84-8b6cc8a97034</a>. Formatted as a Frictionless Data package.
Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 3. Continued. RAxML tree based on the concatenated 83 nuclear loci of the LEO dataset. Numbers on the branches are bootstrap values (BS)>50%; additionally, LPP and quartet support values (QSV) from MSC analysis (see suppl. Fig. S4) are given in the order BS/LLP/QSV for nodes along the backbone of Ochneae. The indicated classification of subfamilies and tribes follows Schneider & al. (2014). Numbers in parentheses after species names correspond to the specimen IDs (only for species with multiple accessions).
Fig 2 in Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)
Fig 2. Chronograms of main sections in Dipterocarpoideae based on plastome (A) and NRC (B) sequences plus outgroups inferred by BEAST 2. Node ages (in Ma) shown at nodes; 95% highest posterior density (HPD) intervals as black bars. All nodes with posterior probability (PP) 1, except nodes with blue circles (PP = 0.83–0.98) and grey circles (PP = 0.56–0.66). Overlay with revised tribal classification: A1: Vaterieae; A2: Dipterocarpeae; A3: Dryobalanopseae; A4: Shoreeae; A5: Doona + Anthoshorea + Neobalanocarpus + Hopea clade; A6: Shorea sect. Doona; A7: S. sect. Anthoshorea; A8: Richetioides + Parashorea + Rubroshorea clade; A9: S. sect. Richetioides; A10: S. sect. Shorea; A11: S. sect. Rubroshorea; B1: Vaterieae; B2: Dipterocarpeae; B3: Dryobalanopseae; B4: Shoreeae; B5: sect. Richetioides; B6: Shorea + Rubroshorea + Parashorea + Anthoshorea + Neobalanocarpus + Hopea clade; B7: S. sect. Shorea; B8: S. sect. Rubroshorea; B9: S. sect. Anthoshorea; B10: Neobalanocarpus + Hopea clade. Geological time scale shown in millions of years.
Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.
Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
Data from: A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies.
Background: Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa on a phylogenomic scale, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising >800 exon sequences was subsequently used for phylogenetic reconstructions. Results: Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei. Conclusions: Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveal that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Two further characters associated to the swim bladder remain possible apomorphies, as their status could not be evaluated, since Alepocephaliformes do not have this structure. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.
Data from: An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating
Most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. Building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. Using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and genetic data, showed that members of the Halobacteriales and Thermococcales are able to metabolize chitin. Ancestral state reconstruction combined with phylogenetic analysis of the genes underlying chitin degradation predicted that the ancestors of these two groups were also likely able to metabolize chitin or chitin-related compounds. These two clades were therefore assigned a maximum age of 1.0 Ga (when chitin likely first appeared). Similar analyses also predicted that the ancestor to the Sulfolobus solfataricus-Sulfolobus islandicus clade was able to metabolize phenol using catechol dioxygenase, so this clade was assigned a maximum age of 475 Ma. Inferred ages of archaeal clades using relaxed molecular clocks with the new age constraints were consistent with those inferred with the oxygen age constraints. This work expands our current toolkit to include Paleoproterozoic, Neoproterozoic, and Paleozoic age constraints, and should aid in our ability to phylogenetically reconstruct the antiquity of a wide array of microbial clades and their associated morphological and biogeochemical traits, spanning deep geologic time. Such hypotheses-although built upon evolutionary inferences-are fundamentally testable.
Data from: Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda
The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we simultaneously reconstructed the phylogenetic relationships and the absolute times of divergences among the arthropods. Simulations were used to test whether our analysis could distinguish between alternative Cambrian explosion scenarios with increasing levels of autocorrelated rate variation. Our analyses support previous phylogenomic hypotheses and simulations indicate a Precambrian origin of the arthropods. Our results provide insights into the 3 independent colonizations of land by arthropods and suggest that evolution of insect wings happened much earlier than the fossil record indicates, with flight evolving during a period of increasing oxygen levels and impressively large forests. These and other findings provide a foundation for macroevolutionary and comparative genomic study of Arthropoda.
Data from: Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae
Background: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation, occurring in aquatic, terrestrial and aeroterrestrial environments. Because a reliable backbone phylogeny is essential to understand the evolutionary history of the Trebouxiophyceae, we sought to identify the relationships among the major trebouxiophycean lineages that have been previously recognized in nuclear-encoded 18S rRNA phylogenies. To this end, we used a chloroplast phylogenomic approach. Results: We determined the sequences of 29 chlorophyte chloroplast genomes and assembled amino acid and nucleotide data sets derived from 79 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The amino acid- and nucleotide-based phylogenies inferred using maximum likelihood and Bayesian methods and various models of sequence evolution revealed essentially the same relationships for the trebouxiophyceans. Two major groups were identified: a strongly supported clade of 29 taxa (core trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a clade comprising the Chlorellales and Pedinophyceae that represents a basal divergence relative to the former group. The core trebouxiophyceans form a grade of strongly supported clades that include a novel lineage represented by the desert crust alga Pleurastrosarcina brevispinosa. The assemblage composed of the Oocystis and Geminella clades is the deepest divergence of the core trebouxiophyceans. Like most of the chlorellaleans, early-diverging core trebouxiophyceans are predominantly planktonic species, whereas core trebouxiophyceans occupying more derived lineages are mostly terrestrial or aeroterrestrial algae. Conclusions: Our phylogenomic study provides a solid foundation for addressing fundamental questions related to the biology and ecology of the Trebouxiophyceae. The inferred trees reveal that this class is not monophyletic; they offer new insights not only into the internal structure of the class but also into the lifestyle of its founding members and subsequent adaptations to changing environments.
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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.