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Supporting data sets for "Estimating Carbon Fixation of Plant Organs for Afforestation Monitoring using a Process-based Ecosystem Model and Ecophysiological Parameter Optimization". (the survey of tree breast diameter and tree height in 11-year old Eucommia ulmoides plantation, values of simulation results used in figures and tables.)
<p>Supporting data sets for Miyauchi et al., Ecology and Evolution, 2019 (accepted).</p> <p>The files store: </p> <p>(1) The survey of tree breast diameter and tree height in <em>Eucommia ulmoides</em> plantation<em>.</em> The ring and stem analysis and dry weight of seven harvested sample trees in the plantation.</p> <p>(2) Values of optimization result used fig.7.</p> <p>(3) Values of prediction result used fig.8. and table 4.</p> <p>(4) Values of optimized parameters by optimization methods, parameter range and constrain.</p>
Supplementary material 1 from: Motloung R, Robertson M, Rouget M, Wilson J (2014) Forestry trial data can be used to evaluate climate-based species distribution models in predicting tree invasions. NeoBiota 20: 31-48. https://doi.org/10.3897/neobiota.20.5778
Current and potential distributions of sixteen species that are not widespread in southern Africa arranged on the basis of their suitable range size : a) Acacia paradoxa, b) A. cultriformis, c) A. falciformis, d) A. pendula, e) A. rubida, f) A. stricta, g) A. retinodes, h) A. fimbriata, i) A. aneura, j) A. viscidula, k) A. acuminata, l) A. adunca, m) A. binervata, n) A. schinoides, o) A. prominens, p) A. mangium. The grey shading indicates areas that SDMs have identified as suitable by SDMs while the white ones are unsuitable.
Fig. 4. Maximum likelihood tree for 43 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 4. Maximum likelihood tree for 43 species of Lymantria based all substitutions of CO I gene (Bootstrap support are shown at the nodes; ID=specimens from Indonesia).
Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019) in Variability of the gene cyt b in the Korean field mouse Apodemus peninsulae Thomas, 1906 - a reservoir host of AMRV in the Khasansky District of Primorsky Krai
Рис. 1. ФиΛогенетические Αеревья хантавируса AMRV и его прироΑного носитеΛя восточноазиатской мыши Apodemus peninsulae Thomas, 1906. А. ФиΛогенетическое Αерево восточноазиатской мыши Apodemus peninsulae, построенное метоΑом «максимаΛьного правΑопоΑобия» (ML) и поΛученное на основе анаΛиза участка гена цитохрома b мтΔНК (744 п.н.). В узΛах ветвΛения указаны бутстреп-поΑΑержки, рассчитанные ΑΛя 1000 повторов. Цветными Λиниями обозначены фиΛогенетические Λинии: Αве Китайские (зеΛеный), Корейская «Korea» (синий), Амурская «Amur» (красный). ПоΛужирным шрифтом выΑеΛены собственные образцы. Названия образцов из GenBank/NCBI быΛи сокращены; B. ФиΛогенетическое Αерево из работы Α. Н. Яшиной с ΑопоΛнениями, построенное метоΑом «бΛижайшего сосеΑа» (NJ) на основе посΛеΑоватеΛьностей фрагмента М-сегмента (2737–2980 н.п.) генома хантавирусов. В узΛах ветвΛения указаны бутстреппоΑΑержки, рассчитанные ΑΛя 1000 повторов. Жирным выΑеΛены иссΛеΑованные РНК изоΛяты (Яшина 2012; Яшина и Αр. 2019) Fig. 1. Phylogenetic trees of AMRV and its natural reservoir host — the Korean field mouse Apodemus peninsulae Thomas, 1906. A. Phylogenetic tree of the Korean field mouse Apodemus peninsulae constructed by the "maximum likelihood" method (ML). The data are obtained from the analysis of the cytochrome b mtDNA gene fragments (744 bp). Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. Colored lines indicate phylogenetic lines: two Chinese (green), Korea (blue), and Amur (red). Own samples are highlighted in bold. The names of the samples from GenBank/NCBI have been shortened; B. Phylogenetic tree from L. N. Yashina's work with additions constructed by the neighbour joining method (NJ). It is based on the sequences of an M-segment fragment (2737–2980 bp) of the hantavirus genome. Bootstrap supports calculated for 1,000 repeats are indicated in the branching nodes. The researched RNA isolates are highlighted in bold (Yashina 2012; Yashina et al. 2019)
Fig. 5. Maximum likelihood tree for 10 in Molecular phylogeny of Indonesian Zeuzera (Lepidoptera: Cossidae) wood borer moths based on CO I gene sequence
Fig. 5. Maximum likelihood tree for 10 species of Zeuzera based on all substitution of CO I gene (Bootstrap support are shown ath the nodes).
Figure 7. Generated Tree Example-Generative Learning Objects Instantiated with Random Numbers Based Expressions
<p>In this subsection we give an example of a model instantiation. We describe the instantiation<br> process for all the symbols in the AGLO model. The nNoOfElements symbol was instantiated with<br> the generated value of 10. The tabKeys symbol was instantiated with the [A,B,C,D,E,F,G,H,I]<br> generated array. The tree symbol was instantiated with a ”Tree” object built with arguments equal<br> with previously instantiated symbols. Class ”Tree” is part of the auxiliary JavaScript library.The treeSVG symbol was assigned to the tree SVG string representation obtained by a method call and<br> is depicted in figure 7.</p>
Text-fig. 6. Most parsimonious tree obtained after addition of Acaciaephyllum to the data set of Doyle (2008), with modifications discussed in the text, and with relationships of other taxa fixed with a backbone constraint tree based on results of Doyle (2008). Relative parsimony of alternative positions of Acaciaephyllum is indicated as in Text-fig. 2. Gnet = Gnetales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 6. Most parsimonious tree obtained after addition of Acaciaephyllum to the data set of Doyle (2008), with modifications discussed in the text, and with relationships of other taxa fixed with a backbone constraint tree based on results of Doyle (2008). Relative parsimony of alternative positions of Acaciaephyllum is indicated as in Text-fig. 2. Gnet = Gnetales.
Text-fig. 2. Representative most parsimonious trees obtained after addition of Liliacidites to (A) the D&E tree (Text-fig. 1) and (B) the J/M tree, with relationships among major clades based on the plastid genome analyses of Jansen et al. (2007) and Moore et al. (2007). Thicker lines indicate all most parsimonious (MP), one step less parsimonious (MP+1), and two step less parsimonious (MP+2) positions for Liliacidites. Abbreviations as in Text-fig. 1. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 2. Representative most parsimonious trees obtained after addition of Liliacidites to (A) the D&E tree (Text-fig. 1) and (B) the J/M tree, with relationships among major clades based on the plastid genome analyses of Jansen et al. (2007) and Moore et al. (2007). Thicker lines indicate all most parsimonious (MP), one step less parsimonious (MP+1), and two step less parsimonious (MP+2) positions for Liliacidites. Abbreviations as in Text-fig. 1.
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Figure. Interferon alpha-A based phylogenetic tree (neighbor joining method) constructed by MEGA 6.1 for Punjab urial in comparison with other mammalian species sequences available from GenBank (NCBI). in Characterization of interferon alpha of major histocompatibility complex class I in Punjab urial (Ovis vignei punjabiensis)
Figure. Interferon alpha-A based phylogenetic tree (neighbor joining method) constructed by MEGA 6.1 for Punjab urial in comparison with other mammalian species sequences available from GenBank (NCBI).
Figure 1. A neighbour-joining tree using 604 cytochrome C oxidase sub-unit I in Phylogenetic relationship among slender loris species (Primates, Lorisidae: Loris) in Sri Lanka based on mtDNA CO1 barcoding
Figure 1. A neighbour-joining tree using 604 cytochrome C oxidase sub-unit I (CO1) sequences from 7 different slender loris (Loris) taxas, rooted using slow loris (Nycticebus) sequences deposited in the GenBank.
Prediction of Humpback Whale Sighting Zones based on Environmental Factors using Tree-based Algorithms
<p>This is the datased used in the paper: Prediction of Humpback Whale Sighting Zones based on Environmental Factors using Tree-based Algorithms</p>
Code and data for molecular dating benchmark based on real and simulated Primates gene trees
<p>Benchmark of molecular clock dating applied to single gene trees separately, whose results are described in “Factors influencing the accuracy and precision in dating single gene trees” by Guillaume Louvel and Hugues Roest Crollius.</p> <ol> <li>Real Primates gene trees are analyzed to identify what characteristics of a gene tree are related to the precision of dating; </li> <li>alignments are also simulated on the tree of Primates to measure the accuracy of dating under controlled parameters such as the degree of rate variation and the length of the alignment.</li> </ol> <p><strong>Content</strong></p> <p><code>Louvel_Accuracy-dating_results_2024.tar.gz</code>:<br> - <code>notebook/</code>: statistical analyses in Python;<br> - <code>outputs/</code>: html reports with figures/tables resulting from the analysis;<br> - <code>lib/</code>: required libraries.<br> - <code>data/</code>: intermediate data needed for the final analysis (dates, gene tree features);</p> <p><code>Louvel_Accuracy-dating_dating-source_2024.tar.gz</code>:<br> - <code>dating-source/</code>: input data and config files necessary to reproduce <code>data</code>;</p> <p><code>Louvel_Accuracy-dating_raw-data-preparation_2024.tar.gz</code>:<br> - <code>raw-data-preparation/</code>: raw data and steps to produce <code>dating-source</code>.<br><br><strong>Requirements</strong><br><br>This code requires the libraries developed in the lab for this project,<br>available at <a href="https://github.com/DyogenIBENS/">github.com/DyogenIBENS/</a>, but also included here in <code>lib/</code>.<br><br>- <a href="https://github.com/DyogenIBENS/Phylorgs">Phylorgs</a><br>- <a href="https://github.com/DyogenIBENS/LibsDyogen_py3">LibsDyogen_py3</a><br>- <a href="https://github.com/DyogenIBENS/ToolsDyogen_py3">ToolsDyogen_py3</a>.</p>
Fig. 3. The simplified phylogenetic tree modified from Figs. 1 & 2 in Systematics of the family Ocypodidae Rafinesque, 1815 (Crustacea: Brachyura), based on phylogenetic relationships, with a reorganization of subfamily rankings and a review of the taxonomic status of Uca Leach, 1814, sensu lato and its subgenera
Fig. 3. The simplified phylogenetic tree modified from Figs. 1 & 2, with number of species beside or below the taxa/group. The gray boxes mean the genera are not fiddler crabs.
Figure 4. Phenetic tree with 25 in A web based tool to merge geometric morphometric data from multiple characters
Figure 4. Phenetic tree with 25 dung beetles based on Procrustes distances, which are computed from the merged geometric morphometric data from characters of the epipharynx, right mandible, pronotum, elytra, hind wing, and metendosternite in lateral and dorsal view (totally 649 landmarks). Abbreviations for the tribe names: AT—Ateuchini, CO—Coprini, DE—Deltochilini, GY— Gymnopleurini, ON—Oniticellini, OP—Onthophagini, OT—Onitini, SC—Scarabaeini, SI—Sisyphini.
Text-fig. 7. Number of required character state changes under parsimony (steps) for various positions of Mugideiriflora portugallica, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 7. Number of required character state changes under parsimony (steps) for various positions of Mugideiriflora portugallica, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014).
Text-fig. 8. Number of required character state changes under parsimony (steps) for various positions of Lambertiflora elegans, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 8. Number of required character state changes under parsimony (steps) for various positions of Lambertiflora elegans, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014).
Text-fig. 9. Number of required character state changes under parsimony (steps) for various positions of Atlantocarpus virginiensis, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014). in Multiparted, Apocarpous Flowers From The Early Cretaceous Of Eastern North America And Portugal
Text-fig. 9. Number of required character state changes under parsimony (steps) for various positions of Atlantocarpus virginiensis, based on the Doyle and Endress character matrix and backbone tree (Doyle and Endress 2000, 2014).
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 % complete dataset, consisting of 4561 loci. Circles on the branch represent a local posterior probability support of 0.95 to 1.0. Abbreviations – AT – Atractaspidinae, CL – Cyclocoridae, EL – Elapidae, LM – Lamprophiinae, MC – Micrelapidae fam. nov., OG – outgroup, PD – Pseudaspidinae, PR – Prosymninae, PS – Psammophiinae, PX – Pseudoxyrhophiinae.
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.