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230 results for “phylogenetic scale”
Scale-dependent drivers of the phylogenetic structure and similarity of tree communities in northwestern Amazonia
<p><span><span><span><span><span><span><span><span><span><span><span><span>1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic relatedness and low phylogenetic turnover. ii) Geographical barriers triggered dispersal limitation, causing high local and subregional phylogenetic clustering and high regional phylogenetic turnover. iii) Edaphic properties and flooding were negatively associated to stem size and determined the tree phylogenetic structure and turnover at local and regional scales in Amazon forests.</span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>3. We found that the extent to which environmental or evolutionary features shaped the phylogenetic structure and phylogenetic similarity of tree communities in NW Amazonia was scale dependent. Specifically, we show that the relative importance of environmental factors increases as spatial scale and species pool decreases. Further, we find that these results are generally robust for both adult and juvenile trees. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><i>Synthesis</i><span><span><span><span><span><span><span><span><span><span><span><span>: Our analysis at the regional (NW Amazon) scale lends support to the idea of Amazonian forests as a large metacommunity</span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span> primarily structured by historical dispersal at large spatial scales with an increasing importance of environmental factors at finer spatial scales. The convergence of ancestral lineages across </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>habitat types </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>may have been due to the relatively recent formation of geographical barriers that promoted local isolation and allopatric speciation.</span></span></span></span></span></span></span></span></span></span></span></span></p>
Supplementary material 1 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639
Figures S1–S5. Additional graphs with result analysis and phylogenetical trees used in data analysis
← Fig. 16. Liscocephala gen.n. and Triunfus gen.n. ♀: L. fumosa: A, C: female terminalia. T. carvalhoi: B, D: female terminalia; E, F: female receptaculum seminis and ausenwand. T. incarnatus: G: female receptaculum seminis and ausenwand. Scale bars = 0.5 mm. in Systematics of the Mecocephala group (Hemiptera: Heteroptera: Pentatomidae) based on a phylogenetic perspective: Inclusion of Hypanthracos, description of three new genera, and redescription of Ogmocoris
← Fig. 16. Liscocephala gen.n. and Triunfus gen.n. ♀: L. fumosa: A, C: female terminalia. T. carvalhoi: B, D: female terminalia; E, F: female receptaculum seminis and ausenwand. T. incarnatus: G: female receptaculum seminis and ausenwand. Scale bars = 0.5 mm.
→ Fig. 5. Hypanthracos meridionalis Grazia & Campos, 1996: A–F: male terminalia: A – D: dorsal; B – E: posterior: C – F: ventral; G – I: male genitalia: G: dorsal; H: lateral; I: ventral; J: female terminalia; K: female receptaculum seminis and ausenwand. Scale bars: A – F = 1.0 mm; G – I: 0.01 mm; J – K = 0.5 mm. in Systematics of the Mecocephala group (Hemiptera: Heteroptera: Pentatomidae) based on a phylogenetic perspective: Inclusion of Hypanthracos, description of three new genera, and redescription of Ogmocoris
→ Fig. 5. Hypanthracos meridionalis Grazia & Campos, 1996: A–F: male terminalia: A – D: dorsal; B – E: posterior: C – F: ventral; G – I: male genitalia: G: dorsal; H: lateral; I: ventral; J: female terminalia; K: female receptaculum seminis and ausenwand. Scale bars: A – F = 1.0 mm; G – I: 0.01 mm; J – K = 0.5 mm.
A multi-tiered sequence capture strategy spanning broad evolutionary scales: application for phylogenetic and phylogeographic studies of orchids
<p><span><span><span><span><span><span><span><span><span><span><span>With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here we outline a multi-tiered sequence capture strategy aimed at capturing 100's of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative <i>de novo </i>and reference-guided assembly, before target sequence extraction, annotation and alignment, and application of a homology-aware <i>k-mer</i> block phylogenomic approach, prior to phylogenetic inference using maximum-likelihood. Our evaluation considered 87 taxa in two test datasets: 67 samples spanning the tribe, and 72samples involving 24 closely related <i>Caladenia</i> species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1–5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous <i>k</i>-mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customised multi-tiered sequence capture strategy, in combination with promising yet under-utilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales
The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter- and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland-forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species-trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co-occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community assembly at broader scales.
FIGURE 2. Ateleidea spinosa, genital morphology. A, epigynum ventral view. B, epigynum ventral view cleared. C, epigynum dorsal view cleared. D, male pedipalp ventral view cleared. E male pedipalp expanded. Scale bars 0.2 in Phylogenetic placement and redescription of the spider genus Atelidea Simon, 1895 (Araneae, Tetragnathidae)
FIGURE 2. Ateleidea spinosa, genital morphology. A, epigynum ventral view. B, epigynum ventral view cleared. C, epigynum dorsal view cleared. D, male pedipalp ventral view cleared. E male pedipalp expanded. Scale bars 0.2 mm, A–C same scale, D– E same scale.
FIGURE 1. Ateleidea spinosa, somatic morphology. A, female habitus. B, male habitus. C, female lateral view. D, male cephalothorax frontal view. E, female cephalothorax frontal view. F male femur and metatarsus I. Scale bars 0.5 in Phylogenetic placement and redescription of the spider genus Atelidea Simon, 1895 (Araneae, Tetragnathidae)
FIGURE 1. Ateleidea spinosa, somatic morphology. A, female habitus. B, male habitus. C, female lateral view. D, male cephalothorax frontal view. E, female cephalothorax frontal view. F male femur and metatarsus I. Scale bars 0.5 mm, A–C same scale, D–E same scale.
Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
<p>Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25ºC; daily alternating 25/15ºC for each 12 h). Germination was low with a skewed distribution (mean = 38.9% at 25ºC, and 43.3% at 25/15ºC). One fifth of the species had low (<10%) and slow (4–30d) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6d) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.</p>
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm.
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. SEM images of the studied Coelastrella strains: (A) SYKOA Ch-045-09. (B) SYKOA Ch-047-11. (C) SYKOA Ch-072-17. (D) IRK-A 173. (E) IRK-A 2. Scale bar: 10μm.
FIGURE 3. Begonia nigritarum. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A in Begonia ×dinglensis, a natural hybrid of Philippine Begonia section Baryandra, as evidenced by morphological, phylogenetic and cytological data
FIGURE 3. Begonia nigritarum. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A is 10 cm, B and G are 1 cm, C–E are 0.5 cm, F is 3 cm. [All photos from Ching-I Peng 23858 (HAST).]
FIGURE 2. Begonia camiguinensis. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A in Begonia ×dinglensis, a natural hybrid of Philippine Begonia section Baryandra, as evidenced by morphological, phylogenetic and cytological data
FIGURE 2. Begonia camiguinensis. A. habit. B. inflorescence. C. staminate flower. D. pistillate flower. E. developing capsule. F. leaf, abaxial view. G. rhizome. Scale bars for A is 10 cm, B and G are 1 cm, C–E are 0.5 cm, F is 3 cm. [All photos from Ching-I Peng 23853 (HAST).]
FIGURE. Puccinia klugkistiana on Ligustrum obtusifolium (A–F, N, O, P) and Cleistogenes hackelii (G–N). A. Plant hedges producing spermogonia and aecia in the field. B. Spermogonia on the upper leaf surface. C. Vertical section of an aecium surrounded with peridia. D. Aecia on the lower leaf surface. E. Vertical section of a spermogonium. F. Aeciospores. G. Uredinia on the leaf surface. H. Vertical section of a uredinium. I. Urediniospores. J, K. Telia on the leaf surface. L. Teliospores. M. Urediniospore observed under SEM. N. Vertical section of an uredinium observed under SEM. O. Aecium observed under SEM. P. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C = 100 μm, E, F = 20 μm, H, I = 30 μm, M = 5 μm, P = 10 μm, H, L, O = 40 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia klugkistiana on Ligustrum obtusifolium (A–F, N, O, P) and Cleistogenes hackelii (G–N). A. Plant hedges producing spermogonia and aecia in the field. B. Spermogonia on the upper leaf surface. C. Vertical section of an aecium surrounded with peridia. D. Aecia on the lower leaf surface. E. Vertical section of a spermogonium. F. Aeciospores. G. Uredinia on the leaf surface. H. Vertical section of a uredinium. I. Urediniospores. J, K. Telia on the leaf surface. L. Teliospores. M. Urediniospore observed under SEM. N. Vertical section of an uredinium observed under SEM. O. Aecium observed under SEM. P. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C = 100 μm, E, F = 20 μm, H, I = 30 μm, M = 5 μm, P = 10 μm, H, L, O = 40 μm.
FIGURE. Puccinia cerinthes-agropyrina on Clematis sp. A. Plants producing spermogonia and aecia on the leaves and stems in the field. B. Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Aecia on the stem. E. Aeciospores. F. Aeciospore with verrucose surface observed under SEM. G. Aecium observed under SEM. H. Vertical section of an aecium. Scale bars: C = 20 μm, E, H = 30 μm, F = 5 μm, G = 100 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia cerinthes-agropyrina on Clematis sp. A. Plants producing spermogonia and aecia on the leaves and stems in the field. B. Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Aecia on the stem. E. Aeciospores. F. Aeciospore with verrucose surface observed under SEM. G. Aecium observed under SEM. H. Vertical section of an aecium. Scale bars: C = 20 μm, E, H = 30 μm, F = 5 μm, G = 100 μm.
FIGURE. Puccinia phragmitis on Rumex patientia (A–E, I, K) and Phragmites australis (F–H, J). A, B Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Vertical section of an aecium surrounded with peridia. E. Aeciospores. F, G. Telia on the leaf surface. H. Teliospores. I. Aecium observed under SEM. J. Vertical section of a telium. K. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C, D, E = 30 μm, H = 10 μm, I = 100 μm, J = 20 μm, K = 3 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia phragmitis on Rumex patientia (A–E, I, K) and Phragmites australis (F–H, J). A, B Spermogonia and aecia on the lower leaf surface. C. Vertical section of a spermogonium. D. Vertical section of an aecium surrounded with peridia. E. Aeciospores. F, G. Telia on the leaf surface. H. Teliospores. I. Aecium observed under SEM. J. Vertical section of a telium. K. Aeciospores with various sizes of verrucae on the surface observed under SEM. Scale bars: C, D, E = 30 μm, H = 10 μm, I = 100 μm, J = 20 μm, K = 3 μm.
FIGURE. Puccinia elymi on species of Poaceae. A, B. Telia on the leaf surface. C. Teliospores. D. Vertical section of a telium. Scale bars: C = 30 μm, D = 20 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia elymi on species of Poaceae. A, B. Telia on the leaf surface. C. Teliospores. D. Vertical section of a telium. Scale bars: C = 30 μm, D = 20 μm.
FIGURE. Puccinia miscanthi on Plantago asiatica (A–H) and Miscanthus sacchariflorus (I–Q). A. Plants producing spermogonia and aecia on the leaf surface. B. Spermogonia on the leaf surface. C. Aecia on lower leaf surface. D. Vertical section of a spermogonium. E. Aeciospores. F. Vertical section of an aecium observed under SEM. G. Aeciospores with verrucose surface observed by SEM. H. Vertical section of an aecium surrounded by peridia. I. Plants producing uredinia on the leaf surface in the field. J. Vertical section of an uredinium with paraphyses. K. Urediniospores. L. Uredinia on the leaf surface. M. Uredinium on the leaf surface observed under SEM. N. Urediniospore with echinulate surface observed under SEM. O. Telia on the leaf surface. P. Vertical section of a telium. Q. Teliospores. Scale bars: D, E, K = 20 μm, F, H, M = 100 μm, G = 5 μm, J, P, Q = 30 μm, N = 10 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia miscanthi on Plantago asiatica (A–H) and Miscanthus sacchariflorus (I–Q). A. Plants producing spermogonia and aecia on the leaf surface. B. Spermogonia on the leaf surface. C. Aecia on lower leaf surface. D. Vertical section of a spermogonium. E. Aeciospores. F. Vertical section of an aecium observed under SEM. G. Aeciospores with verrucose surface observed by SEM. H. Vertical section of an aecium surrounded by peridia. I. Plants producing uredinia on the leaf surface in the field. J. Vertical section of an uredinium with paraphyses. K. Urediniospores. L. Uredinia on the leaf surface. M. Uredinium on the leaf surface observed under SEM. N. Urediniospore with echinulate surface observed under SEM. O. Telia on the leaf surface. P. Vertical section of a telium. Q. Teliospores. Scale bars: D, E, K = 20 μm, F, H, M = 100 μm, G = 5 μm, J, P, Q = 30 μm, N = 10 μm.
FIGURE. Puccinia triticina on species of Poaceae. A. Vertical section of an uredinium. Scale bars: A = 30 μm. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Puccinia triticina on species of Poaceae. A. Vertical section of an uredinium. Scale bars: A = 30 μm.
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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)
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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.