Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
24
datasets available to search
ShareScore release 0.9.0
Dataset results
24 results for “branching pattern”
MCR LTER: Coral Reef: 3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals; data for Curtis 2023, Coral Reefs
These data and code were generated in support of the manuscript: Curtis JS, Galvan JW, Primo A, Osenberg CW, and AC Stier, Coral Reefs. We collected manual and photogrammetry-based measurements of coral size and volume to examine which method best described short-term coral growth and links between coral habitat and biodiversity of CAFI (coral-associated fishes and invertebrates). This study was completed between August and December 2019 on an experimental array located in the back reef off the south shore of Moorea, French Polynesia. These data were published in Coral Reefs, analyses and full methods descriptions of this model can be found in the manuscript “3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals”. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
Text-fig. 3. Scanning electron microscope (SEM) images of a charalean oospore (a), and fragments of probable marchantialean liverwort thalli (b–d); Torres Vedras locality, Portugal. a) Apical view of oospore showing the pattern of spiral ridges and grooves resulting from the enclosing cells of the oogonium. b–d) Thallus fragments in probable ventral view showing two rows of imbricate scales and occasional branching of the thallus (d). Specimens, TV38-S174607 (a), TV43-S174655 (b), TV43-S174654 (c), TV43-S174661 (d). Scale bars 1 mm (b–d), 100 Μm (a). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 3. Scanning electron microscope (SEM) images of a charalean oospore (a), and fragments of probable marchantialean liverwort thalli (b–d); Torres Vedras locality, Portugal. a) Apical view of oospore showing the pattern of spiral ridges and grooves resulting from the enclosing cells of the oogonium. b–d) Thallus fragments in probable ventral view showing two rows of imbricate scales and occasional branching of the thallus (d). Specimens, TV38-S174607 (a), TV43-S174655 (b), TV43-S174654 (c), TV43-S174661 (d). Scale bars 1 mm (b–d), 100 Μm (a).
Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification
Open the record for dataset details and reuse information.
FIGURE. Euphorbia parvimedusae in cultivation by P.Pavelka (Czech Republic). A. detail of the subterranean branching pattern with caudex; B. young flowering branch; C. habit in cultivation; D. detail of an inflorescence, cyathia with staminate flowers. Credits: R. van Veldhuisen (A–D). in Taxonomic changes and new species in Malagasy Euphorbia (Euphorbiaceae)
FIGURE. Euphorbia parvimedusae in cultivation by P.Pavelka (Czech Republic). A. detail of the subterranean branching pattern with caudex; B. young flowering branch; C. habit in cultivation; D. detail of an inflorescence, cyathia with staminate flowers. Credits: R. van Veldhuisen (A–D).
FIGURE. Euphorbia mahaboana in habitat, Mahabo. A. branching pattern; B. habit; C. female cyathium, young fruit stage; D. fruit, exceptionally 4-locular (normally 3-locular). Credits: P.E.Berry (A–D). in Taxonomic changes and new species in Malagasy Euphorbia (Euphorbiaceae)
FIGURE. Euphorbia mahaboana in habitat, Mahabo. A. branching pattern; B. habit; C. female cyathium, young fruit stage; D. fruit, exceptionally 4-locular (normally 3-locular). Credits: P.E.Berry (A–D).
FIGURE. Branching patterns of complex thalloid liverworts in Sri Lanka. (A) Terminal innovations (B) Terminal dichotomies (C) Ventral intercalary. in Thalloid Liverworts (Marchantiopsida) of Sri Lanka
FIGURE. Branching patterns of complex thalloid liverworts in Sri Lanka. (A) Terminal innovations (B) Terminal dichotomies (C) Ventral intercalary.
FIGURE 1. Digitaria clarkiae. A. Plant. B. Ligular area. C. Synflorescence branching pattern. D. Spikelet frontal view showing first glume and sterile lemma. E. Spikelet showing second glume. F. Sterile palea. G in Digitaria clarkiae (Paniceae, Panicoideae, Poaceae), a new species with a paniculate synflorescence, and the first record of D. costaricensis from México
FIGURE 1. Digitaria clarkiae. A. Plant. B. Ligular area. C. Synflorescence branching pattern. D. Spikelet frontal view showing first glume and sterile lemma. E. Spikelet showing second glume. F. Sterile palea. G. Fertile floret. From the type (L. Aragón 362, MEXU).
FIGURE 1. Sapium sceleratum. A. Branch. B–C. Acropetiolar glands. D. Leaf margin. E–F. Leaf shapes and veins pattern. G. Inflorescence base. H. Staminate flower. I in Reinstatement of Sapium sceleratum (Euphorbiaceae), an endemic species from Northeast Brazil, and new circumscription of Sapium argutum
FIGURE 1. Sapium sceleratum. A. Branch. B–C. Acropetiolar glands. D. Leaf margin. E–F. Leaf shapes and veins pattern. G. Inflorescence base. H. Staminate flower. I. Pistillate flower showing calyx covering more than half of the length of the ovary. J. Pistillate sepal. A–C. A. M. Miranda 3273 (HST). D. A. M. Miranda 4214 (HST). E–H. Carvalho Sobrinho et al. 1840 (HVASF).
FIGURE 2. Sapium argutum. A. Branch. B–C. Acropetiolar glands. D. Leaf shape and veins pattern. E–F. Leaf margin. G. Inflorescence apex. H. Inflorescence base. I. Staminate flower. J. Pistillate flower. K. Pistillate sepal. L. Seed. A–L. W. Cordeiro 780 in Reinstatement of Sapium sceleratum (Euphorbiaceae), an endemic species from Northeast Brazil, and new circumscription of Sapium argutum
FIGURE 2. Sapium argutum. A. Branch. B–C. Acropetiolar glands. D. Leaf shape and veins pattern. E–F. Leaf margin. G. Inflorescence apex. H. Inflorescence base. I. Staminate flower. J. Pistillate flower. K. Pistillate sepal. L. Seed. A–L. W. Cordeiro 780 (PEUFR).
FIGURE 3. A–E Chusquea fruticosa. A. Habitat. B. Habit. C. Culm leaves. D. Branch complements and foliage leaves. E. Synflorescences and foliage leaves. F–J Chusquea caparaoensis. F. Habitat and habit. G. Branching pattern and foliage leaves. H. Synflorescence and foliage leaves. I. Dead culms. J in Two new species of Chusquea subg. Swallenochloa (Poaceae: Bambusoideae: Bambuseae) from Minas Gerais, Brazil, and complete description of C. caparaoensis
FIGURE 3. A–E Chusquea fruticosa. A. Habitat. B. Habit. C. Culm leaves. D. Branch complements and foliage leaves. E. Synflorescences and foliage leaves. F–J Chusquea caparaoensis. F. Habitat and habit. G. Branching pattern and foliage leaves. H. Synflorescence and foliage leaves. I. Dead culms. J. Seedling. Photos by Evandro Pianissola.
FIGURE 3. Rhipidocladum cordatum. A. Branch complement, B. Apsidate branching pattern, C. Culm leaf, D in Three new species of Rhipidocladum (Poaceae: Bambusoideae: Arthrostylidiinae) from South America
FIGURE 3. Rhipidocladum cordatum. A. Branch complement, B. Apsidate branching pattern, C. Culm leaf, D. Close up of culm leaf blade base showing "pleats" (a folding or puckering of the blade tissue across the venation) illustrated with stippling, E. Foliage leaf ligular area, F. Synflorescence, G. Spikelet. Illustration by Anna B. Gardner; A, C, D, and E based on Clark et al. 1092, B based on Clark & Asimbaya 1415, F and G based on Young 164.
FIGURE. Growth pattern of shrub species. A. Erect, cespitose in Ch. pachyclada. B. Decumbent in Ch. ustulata. C. Branched in Ch. claussenii. D. Not branched in Ch. claussenii. in Taxonomic review of Chamaecrista sect. Absus subsect. Absus ser. Paniculatae (Benth.) H.S. Irwin & Barneby (Leguminosae, Caesalpinioideae)
FIGURE. Growth pattern of shrub species. A. Erect, cespitose in Ch. pachyclada. B. Decumbent in Ch. ustulata. C. Branched in Ch. claussenii. D. Not branched in Ch. claussenii.
FIGURE. Growth patterns of tree species and texture of their branches. A. Small tree erect lax canopy in Ch. orbiculata. B. Small tree with little branched stem in Ch. tocantinensis. C. Small tree with very branched stem in Ch. trichortyrsus. D. Stems with bark cerous in Ch. claussenii. E. Stems with bark longitudinally fissured in Ch. celiae. in Taxonomic review of Chamaecrista sect. Absus subsect. Absus ser. Paniculatae (Benth.) H.S. Irwin & Barneby (Leguminosae, Caesalpinioideae)
FIGURE. Growth patterns of tree species and texture of their branches. A. Small tree erect lax canopy in Ch. orbiculata. B. Small tree with little branched stem in Ch. tocantinensis. C. Small tree with very branched stem in Ch. trichortyrsus. D. Stems with bark cerous in Ch. claussenii. E. Stems with bark longitudinally fissured in Ch. celiae.
Data from: Patterns of cranial shape diversification during the phylogenetic branching process of New World monkeys (Primates: Platyrrhini)
Open the record for dataset details and reuse information.
Data from: Disentangling the fundamental branching patterns of phylogenetic divergence to refine eco-phylogenetic analyses
Aim: Previous studies have shown that phylogenetic divergence (i.e. the average phylogenetic displacement between species in a community) is highly sensitive to the underlying branching patterns of phylogenies, suggesting that there is a need to integrate both facets of phylogenic information to obtain a better understanding of assemblage structure. Here, we formally conceptualize the three fundamental branching patterns that can drive phylogenetic divergence, and propose a method to identify their signature in the communities based on the MPD (mean pairwise distance) metric. Location: Global. Taxa: All. Methods: Our approach consists on the joint interpretation of two MPD-derived metrics that summarize the differential contribution of individual phylogenetic branches to the observed divergence, which serves to evaluate to what extent the later emerges from contrasting branching patterns. We conduct simulation analyses to compare our two metrics with eight classical descriptors of phylogenetic structure, and use multi-strata tropical plant communities along a gradient of land-use intensity (LUI) to further illustrate our method. Results: As expected, our metrics correlated to some extent with the classical descriptors of phylogenetic structure, although the relationships were complex and varied systematically with species richness and the specific combination of metric values considered. Consequently, the information provided by our two indexes was only partially captured by their most correlated classical descriptors. We detected differential signatures of the fundamental branching patterns in our real-world dataset, either across vegetation strata and also within strata along the LUI gradient, which provided greater insight into potential assembly mechanisms. Main conclusions: While the sole use of phylogenetic divergence may lead to spurious interpretations in eco-phylogenetic studies, our approach can help to obtain a better understanding of assemblage structure by systematically analyzing phylogenetic divergence in the light of its fundamental branching patterns.
Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?
Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion.
Rupture pattern exposed by trenches on western and eastern branches of the Xiaojiang Fault zone
<p>Datas online are directly used in the research. </p>
Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?
Open the record for dataset details and reuse information.
Data from: Disentangling the fundamental branching patterns of phylogenetic divergence to refine eco-phylogenetic analyses
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.