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Figure 5 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 5. Amphibioplana onnisi. Habitus of live specimens from the Grutta 'e Pauli Cave. A, specimen with constriction just behind copulatory apparatus; B, C, anterior portion of specimen with regenerating blastema (rb) at the margin of the prepharyngeal part of the body; D, specimen with caudal tip located just behind the pharynx, suggesting a recent postpharyngeal fission; E, specimen with caudal tip located just behind the copulatory apparatus (ca), suggesting a recent caudal fission; F, specimen with a regenerating blastema behind the copulatory apparatus. Scale bars not available.
Figure 4 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 4. Amphibioplana onnisi. Habitat in freshwater environments. A, entrance of Grutta 'e Pauli Cave; B, collection site in Grutta 'e Pauli Cave; C, collection site in San Pietro Cave; D, collection site in Istirzili Cave. Details on precise locations of the sampling sites in the caves are omitted for reasons of species protection.
Figure 2 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 2. Maximum-likelihood tree inferred from the concatenated dataset, including the filtered 18S and 28S alignments (Table 2) of representatives of the various suborders of the Tricladida. Values at nodes correspond to UFB/SH-aLRT/PP; –: PP values below 0.5. Scale bar: number of substitutions per nucleotide position.
Figure 1 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 1. Geographic distribution of Amphibioplana onnisi in the Mediterranean region. Rectangular inset corresponds with area enlarged to right-hand side, showing the island of Sardinia. Filled black circles indicate location of caves from which populations were sampled; green areas indicate the karst regions.
Figure 12. Amphibioplana onnisi. CGAS Pla 24.5 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 12. Amphibioplana onnisi. CGAS Pla 24.5, sagittal reconstruction of the copulatory apparatus; anterior to the left.
Figure 15 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 15. Amphibioplana onnisi. Photomicrographs of the copulatory apparatus. A, CGAS Pla 19.1b, sagittal section showing copulatory bursa (cb), bursal canal (bc) with its diverticulum (di), and common oviduct (cod); anterior to the left; B, RMNH.VER. 19957.a, sagittal section showing copulatory bursa (cb), penis papilla (pp), genital atrium (ga), cup-shaped chamber (csc), common oviduct (cod), and right oviduct (rod); anterior to the left.
Root anatomy helps to reconcile observed root trait syndromes in tropical tree species
<p>Studying the organization of functional traits in plant leaves and stems has revealed notable patterns linking function and form; however, evidence of similarly robust organization in root tissues remains controversial. We posit that anatomical traits in roots can provide insight on the overall organization of the root system. We hypothesize that A) size variation in the tissue outside the stele relates in a non-linear fashion with functional traits associated with direct resource uptake, including a negative relationship with root architectural traits; and B) similar relationships detected in tropical areas also hold true in other biomes.</p> <p>We address our hypotheses using empirical data from 24 tropical tree species in French Guiana, including anatomical measurements in first order roots, and functional trait description for the entire fine root system. In addition, we compiled a global meta-analysis of root trait with 500+ forest species across tropical, subtropical and temperate forests.</p> <p>Our results supported the expected non-linear relationships between cortical size and morphological traits, and a negative linear trend with architectural traits. We confirmed a global negative relationship between SRL, diameter and tissue density, suggesting similar anatomical constraints in root systems across woody plants. However the importance of factors vary across biomes, possibly related to the unequal phylogenetic representation of families across latitudes.</p> <p>Our findings imply that the rhizocentric hypothesis can be a valuable approach to understand fine root trait syndromes and the evolution of absorptive roots in vascular plants.</p>
FIGURE 1. Phylogenetic tree obtained inferred from 69 taxa and 4287 in Dothidea kunmingensis, a novel asexual species of Dothideaceae on Jasminum nudiflorum (winter jasmine) from Southwestern China
FIGURE 1. Phylogenetic tree obtained inferred from 69 taxa and 4287 sites of a combined SSU, LSU, ITS, tub2 and tef1-α sequence dataset. Numerical values at the nodes indicate maximum likelihood bootstrap support (MLBS) and posterior probabilities (PP) in this order. Bootstrap support values for ML higher than 70 % and PP higher than 0.95 are indicated at the node. Ex-type strains are in bold font; the newly generated sequence is in blue bold font.
FIGURE. Basidiocarps of species of Agaricales in Panama. a. Asterophora parasitica (PAN180) on decayed basidiocarp of Russula sp. b–c. Campanophyllum probiscideum. b. On bark of a standing tree (KaiR434). c. From above and below (KaiR434). d–e. Rhodocollybia tablensis. d. (KaiR484). e. (PAN238). f. Cantharocybe brunneovelutina (PAN260). g. Pluteus hongoi (PAN413). h. Tetrapyrgos atrocyanea (KaiR395). Bars a = 1 cm, b, c, f, g = 2 cm, d, e = 5 cm, h = 0.5 cm. a, f, g Photos by H. Lotz-Winter. b, c, d, h Photos by K. Reschke. e Photo by O. Koukol. in New and interesting species of Agaricomycetes from Panama
FIGURE. Basidiocarps of species of Agaricales in Panama. a. Asterophora parasitica (PAN180) on decayed basidiocarp of Russula sp. b–c. Campanophyllum probiscideum. b. On bark of a standing tree (KaiR434). c. From above and below (KaiR434). d–e. Rhodocollybia tablensis. d. (KaiR484). e. (PAN238). f. Cantharocybe brunneovelutina (PAN260). g. Pluteus hongoi (PAN413). h. Tetrapyrgos atrocyanea (KaiR395). Bars a = 1 cm, b, c, f, g = 2 cm, d, e = 5 cm, h = 0.5 cm. a, f, g Photos by H. Lotz-Winter. b, c, d, h Photos by K. Reschke. e Photo by O. Koukol.
FIGURE 2. Disepalum rawagambut. A in Disepalum rawagambut (Annonaceae), a new tree species from peat swamp forest of Sumatra, Indonesia
FIGURE 2. Disepalum rawagambut. A. Flower with pedicel (side view). B. Flower (top view). C. Flower (side view). D. Infructescence. E. Carpophore and monocarp. F. Immature monocarp (longitudinal section). G. Mature monocarp (longitudinal section) and seeds. All photos by A. Randi from the holotype (Randi GB-035).
FIGURE 1. Disepalum rawagambut. A in Disepalum rawagambut (Annonaceae), a new tree species from peat swamp forest of Sumatra, Indonesia
FIGURE 1. Disepalum rawagambut. A. Trunk and stilt roots on old tree. B. Twig with flowers and infructescence. C. Close-up of twig. D. Adaxial surface (upper) and abaxial surface (below) of leaves. All photos by A. Randi from the holotype (Randi GB-035).
FIGURE 2. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 2. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Tricholomopsis species. ML bootstrap (BS>50%) are shown above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
FIGURE 1. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 1. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Boletinellus species. ML bootstrap (BS>50 %) are indicated above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
Tropical forest restoration in the Eastern Himalaya: Evaluating early survival and growth of native tree species
<p>Asian tropical forests have among the highest rates of forest loss in the world. Ecological restoration is a vital step for biodiversity maintenance and climate change mitigation. For restoration practice, evaluation of species performance at early stages is crucial to avoid failure of the efforts and for screening species suitable to a region. Though the long-term performance of restoration plantings has been well-documented, few studies have evaluated the performance during the establishment of the planted saplings, especially in South and Southeast Asia. Restoration efforts in Northeast India, a region experiencing high forest loss, is limited by the lack of species-specific data on survival and growth. We compared inter-specific variation in seasonal survival and growth rates (diameter and height) for multiple native rainforest species from this region. We planted 3022 saplings of 50 species at a degraded open forest site. After 18 months, sapling survival varied between 9.1–94.3% for 32 species, and only six species showed "excellent" survival after 18 months. Eight out of 17 species that were tested for seasonal variation in survival showed significant differences in survival between seasons. While the diameter growth rate varied for species between seasons, the height growth rate was different between both species and season, but the interaction term between species and season was not significant. Certain animal-dispersed, medium to large-seeded primary forest species performed well and are vital for future restoration efforts in this region.</p>
◂Fig. 2 Maximum likelihood trees. A Tree obtained when analysing 18S data set. B Tree obtained when analysing 28S data set. C Tree obtained when analysing COI data set. D Tree obtained when analysing 16S data set. Bootstrap support values below nodes. Syllis and Typosyllis species as they were originally described in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan
◂Fig. 2 Maximum likelihood trees. A Tree obtained when analysing 18S data set. B Tree obtained when analysing 28S data set. C Tree obtained when analysing COI data set. D Tree obtained when analysing 16S data set. Bootstrap support values below nodes. Syllis and Typosyllis species as they were originally described
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic relationships among species on Poaceae shown with synoptic phylogenetic tree constructed by MP method based on ITS+28S regions of rDNA. Same color branches show phylogenetic groups. 0, I: Spermogonial and aecial host genus.
Sapwood area~DBH allometries for 14 common tree species in a successional tropical forest in Thailand
<p>Sapwood area is an important parameter for estimating canopy transpiration in the forest water cycle. However, sapwood area highly varies across species and forest ecosystems and is difficult to measure directly. Therefore, species- and site-specific allometric equations are needed to estimate the sapwood area of all trees in a forest. Here, we conducted a comprehensive campaign to measure sapwood thickness and to estimate the sapwood area of 14 common tree species in a successional forest in Thailand. These data represent the first comprehensive measurements of sapwood area in south-east Asian successional forests growing under diverse environmental conditions in terms of soil moisture and canopy density. The results show that a power function can significantly explain the relationship between sapwood area and stem size, represented by diameter at breast height (DBH), in all species in both primary and secondary forests. Interestingly, a single equation could describe the sapwood area~DBH relationship in all species and forest stages, except for Dipterocarpus gracilis, an emergent, dominant species in the primary forest. The latter showed slower growth in sapwood area once the trees reached a DBH of ~30 cm. Overall, our results can benefit future studies that estimate canopy transpiration of tropical forests with similar conditions as in our study sites.</p>
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
FIGURE 8 in All in all it's just another branch in the tree: A new species of Acanthocercus Fitzinger, 1843 (Squamata: Agamidae), from Angola
FIGURE 8. Habitat of Acanthocercus ceriacoi sp. nov. at the paratype locality of Zulumongo village, Uíge Province, northern Angola. Photo by Luis M.P. Ceríaco.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.