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Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data
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Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 in A Taxonomic Revision of the Madagascar-Endemic Genus Bemangidia (Sapotaceae), with Description of a Second Species
Figure 1. Phylogenetic tree reconstruction from ASTRAL, using 638 protein-coding genes. Note that ASTRAL calculates only internal branch lengths, and that tip lines are artificially fixed at the same length for all the specimens. The node labels represent ASTRAL support values given as posterior probabilities (PP). Specimen collector's numbers are indicated after the species name, except for Capurodendron and Sapoteae, which appear in Boluda et al. (2022). BioSample numbers for sequence accessions are given in Boluda et al. (2022), except for Bemangidia sp. nov. Randriatafika 813 (BioSample no. SAMN35983425), B. lowryi Gautier 5784 (BioSample no. SAMN35982381), B. lowryi Lowryi et al. 6657 (BioSample no. SAMN35983092), Northia seychellana Bernardi 14641 (BioSample no. SAMN35983402) and Tsebona sp. Andriamiarisoa 2582 (BioSample no. SAMN35983419).
Alignment, ML and MCC trees of dataset A from "Reconstruction of the genetic history and the current spread of HIV-1 subtype A in Germany"
<p>-Alignment and phylogeographic MCC tree of 708 HIV subtype A1 sequences called dataset A in the manuscript "Reconstruction of the genetic history and the current spread of HIV-1 subtype A in Germany"</p> <p>-marked up MCC tree showing SDRM in dataset A</p> <p>-marked up ML tree showing transmission cluster selection in dataset A</p>
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 in A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 are indicated. The tree is rooted with MAC (T. macrosporum) and MAG (T. magnatum)
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 in Trichoderma changiae (Hypocreales), a new species isolated from a native orchid in Taiwan
FIGURE 1. Phylogenetic tree reconstructed from concatenated rpb2 and tef1 sequences using Maximum-likelihood analysis. The new species Trichoderma changiae is highlighted in bold blue. Bootstrap values above 50% from RAxML-HPC2 on XSEDE (left) and posterior probabilities above 0.95 from Bayesian analysis (right) are displayed at the nodes. The scale bar represents 0.05 substitutions per nucleotide position. Trichoderma vulgatum was used as the outgroup. "T" denotes type strains.
FIG. 6. A majority-rule consensus gene tree reconstructed from mtDNA cytochrome oxidase 1 in Redescription and Recognition of Etheostoma cyanorum from Blue River, Oklahoma
FIG. 6. A majority-rule consensus gene tree reconstructed from mtDNA cytochrome oxidase 1 (CO1) sequence data obtained from the Barcode of Life Database (BOLD). Maximum-likelihood (ML) and Bayesian trees had identical topologies. Branch lengths are proportional to inferred mutations. Shading of lineages represents samples from E. whipplei (outgroup) in black, E. cyanorum in gray, and E. radiosum in white. ML bootstrap proportions/ Bayesian posterior probabilities are reported. See Data Accessibility for tree file.
Fig. 13. Neighbour-joining tree reconstructed using 22 in Lasioglossum dorchini (Hymenoptera: Apoidea: Halictidae) a new species of bee from Israel
Fig. 13. Neighbour-joining tree reconstructed using 22 barcode sequences (658bp) of the cytochrome oxidase c subunit I gene for specimens currently identified into the virens/littorale group of species. The tree is drawn to scale, with branch lengths representing p-distances (i.e. proportions of variable sites). Four barcodes sequences (shaded in grey) are used as outgroup for the phylogenetic tree: Lasioglossum morio and L. nitidulum. Each label corresponds to the study code (Table 1) or GenBank accession followed by the species name and the country of collection. The shaded colours on the tree correspond to morphological delineation except for the species identified as Lasioglossum littorale or aff. littorale which are left unshaded. Values at node correspond to bootstrap values (%).
Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth
<p>Project folder for publication "Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth" containing: 1) scripts for data processing, 2) intermediate and final files output by scripts, and 3) RMarkdown files used to perform statistical analyses and generate figures. Descriptions of files, scripts, and folders in README files.</p> <p>Manuscript Abstract:</p> <p><span>As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they <span> </span>are integral to ecosystem health and functioning. Despite microbiomes’ importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration – fungal microbiomes’ importance in “reconstructive” restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature – tree islands – in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared to their natural <span> </span>counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on <span> </span>constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.</span></p>
FIGURE 2 in A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data
FIGURE 2: A. Inflorescence of Lipocarpha chinensis (left) and Ascolepis brasiliensis (right) in Madagascar (picture taken by Marc Reynders); B. Inflorescences of Lipocarpha nana in Madagascar (picture taken by Marc Reynders); C. Inflorescence of Lipocarpha prieuriana (© Marco Schmidt, West African plants - A Photo Guide; photo used with permission of Brunken et al. 2008); D. Lipocarpha micrantha in its natural habitat in the United States (© Arthur Haines, New England Wild Flower Society; photo used with photographer's permission).
FIGURE 7 in A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data
FIGURE 7: Shape of spikelet bracts of Lipocarpha species used in this study (modified from Goetghebeur & Van den Borre 1989). Bars: 1mm. A–D. Clade 1:—A. L. aristulata, B. L. drummondii, C. L. micrantha, D. L. micrantha; E–G. Clade 2:—E. L. albiceps, F. L. comosa, G. Volkiella disticha; H–N. Clade 3:—H. L. microcephala, I. L. filiformis, J. L. cf. filiformis, K. L. salzmannina, L. L. maculata, M. L. prieuriana, N. L. species; O–P. Clade 4:—O. L. leucaspis, P. L. nana; Q–T. Clade 5:—Q. L. hemisphaerica, R. L. chinensis, S. L. constricta, T. L. mexicana (Madagascar); U–V. Clade 6:—U. L. barteri, V. L. humboldtiana; W–X. Clade 7 (flowerbearing glumes instead of spikelet bracts!):—W. L. kernii, X. L. rehmannii. Abbreviations: ap: apical part of spikelet bract; bp: basal part of spikelet bract.
FIGURE 1 in A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data
FIGURE 1: A. Phylogeny of Cyperus s.l., modified from Larridon et al. (2013). Distribution of the segregate genera now included in Cyperus s.l. An asterisk indicates a bootstrap support higher than 75%; B. The segregate genera of Cyperus s.l.
FIGURE 6 in A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data
FIGURE 6: A. New interpretation of the inflorescence of Lipocarpha rehmannii inflorescence. The inflorescence consists of a spikelet of spirally arranged glumes each subtending a flower. B. Old interpretation of the Lipocarpha rehmannii inflorescence (Goetghebeur & Van den Borre 1989). In that interpretation, the inflorescence consists of a spike of highly reduced spikelets with each spikelet subtended by a spikelet bract (blue). Near the base of the nutlet, remnants of a prophyll and glume can be found. Blue = spikelet bract; pink = prophyll; yellow = glume; red = nutlet.
FIGURE 4 in A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data
FIGURE 4: Estimated species tree with coalescent approaches using two chloroplast markers, trnH-psbA and rpl32-trnL and one nuclear marker, ETS1F. Lipocarpha is divided in seven clades, as indicated on the figure. All PP values are shown but we only consider PP values higher then 0.70 as significant. Fig. 4A–E. 3D reconstruction of spikelets (based on Larridon et al. 2013):—A. Spikelet of clades 3–6, B. Spikelet of clade 2, C. Spikelet of clade 1, D. Spikelet of Ascolepis clade, E. Spikelet of clade 7 (Rikliella clade). Blue = spikelet bract; pink = prophyll; yellow = glume; red = nutlet.
FIGURE 3. Tree resulting from a in Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)
FIGURE 3. Tree resulting from a twelve-partition maximum likelihood analysis of the combined 12S–16S and ND2–COI mtDNA genic sequence data. Species with two or more sampled individuals are numbered as in Table 1 for sample location. Filled circles on nodes represent maximum likelihood bootstrap values of ≥ 95. Numbers on branches are bootstrap values <95. Filled diamonds represent branches supported with parsimony bootstrap values ≥ 90, Bayesian posterior probabilities ≥ 0.95, and maximum likelihood bootstrap values ≥ 95.
Figure 4. Maximum-likelihood tree reconstructed from a 4507 in Old views and new insights: taxonomic revision of the Bukovina blind mole rat, Spalax graecus (Rodentia: Spalacinae)
Figure 4. Maximum-likelihood tree reconstructed from a 4507-bp alignment of six mitochondrial sequencesof Spalax species [cytochrome b, NADH1, 12S rRNA, 16S rRNA, tRNA-Leu (UUR), tRNA-Val]. Acomys cahirinus and Nannospalax judaei were used as out-groups. The percentage of trees in which the associated taxa clustered together (after 10 000 replications) is shown next to the branches. The bar represents the number of substitutions per site.
Figure 9. Consensus tree reconstructed from a 489 in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
Figure 9. Consensus tree reconstructed from a 489-bp fragment of the cytochrome c oxidase subunit I gene using Bayesian inference. Node values represent Bayesian posterior probabilities.
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I in Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae)
Figure 1. Best selected tree from a maximum likelihood reconstruction for the cytochrome c oxidase subunit I data set under the general time reversible model with gamma distribution, displaying all compatible groupings and with average branch lengths proportional to numbers of substitutions per site, indicated by the scale bar. Bootstrap support values above 80% are shown below each branch; posterior probabilities above 0.8 from 36 000 sampled trees from the Bayesian analysis are shown above each branch. Support values for within-species relationships are not shown. Filled circles indicate clades (and singlets) identified by the 4¥ rule; open diamonds indicate clades (and singlets) identified by the generalized mixed yule coalescent model. Names refer to the species and the clonal populations.
FIGURE 4. Bayesian posterior probability tree was reconstructed from 16S in A new species of the genus Gracixalus (Amphibia: Anura: Rhacophoridae) from Southern Guangxi, China
FIGURE 4. Bayesian posterior probability tree was reconstructed from 16S ribosomal RNA mitochondrial gene sequences with Philautus aurifasciatus, Kurixalus eiffingeri and K. odontotarsus as outgroups. Maximum-likelihood tree produced nearidentical topology. Two reliability indices are given on nodes: the Bayesian posterior probabilities/the maximum likelihood bootstrap percentages.
FIG. 5.—Phylogenetic tree reconstructed for representative hylodid anurans from a in A New Species of Hŋlodes (Anura, Hylodidae) from Serra do Mar, Southeastern Brazil: The Fourth with Nuptial Thumb Tubercles
FIG. 5.—Phylogenetic tree reconstructed for representative hylodid anurans from a Bayesian inference analysis of the complete 16S mitochondrial gene. Values adjacent to each node are posterior probabilities.
Figure 3 Bayesian inference tree reconstructed from cytochrome b in Fossorial morphotype does not make a species in water voles
Figure 3 Bayesian inference tree reconstructed from cytochrome b sequences of water vole ArVicola. The tree is rooted with 11 species of Arvicolinae: MicrotUS aGreStiS, M. cabrerae, M. SUbterraneUS, M. lUSitanicUS, M. dUodecimcoStatUS, M. arValiS, Neodon irene, N. leUcUrUS, ChionomYS niValiS, C. roberti, and C. GUd. The branching pattern and branch lengths follow the Bayesian analysis, whereas the first and second numbers on the branches correspond to posterior probability values and bootstrap support in the maximum likelihood tree analyses, respectively. Symbols for morphotypes (∆ – fossorial; □ – aquatic) correspond to those in Figure 1 and Table 1.
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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.