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238 results for “Evolutionary relationships”
FIGURE 13. Evolutionary relationships among a in Molecular and morphological systematics of Elysia Risso, 1818 (Heterobranchia: Sacoglossa) from the Caribbean region
FIGURE 13. Evolutionary relationships among a subsample of COI haplotypes from specimens of E. crispata, inferred by Maximum Likelihood. Significant bootstrap values are given adjacent to supported nodes. External morphology of 15 specimens with bolded isolate codes is shown in Fig. 14, with the corresponding panel given in parentheses. Terminals with multiple isolates denote haplotypes sampled more than once; multiple specimens from the same site and year are indicated by two-digit numbers following the corresponding year-site combination, except the total number from two sites is given for the common haplotype sampled in the Dry Tortugas, Dominica and St. Lucia.
Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements
<p>The macroevolutionary consequences of evolving in the deep-sea remain poorly understood and are compounded by the fact that convergent adaptations for living in this environment makes elucidating phylogenetic relationships difficult. Lophiiform anglerfishes exhibit extreme habitat and predatory specializations, including the use of a fin-spine system as a luring device and unique reproductive strategies where parasitic males attach and fuse to females. Despite their notoriety for these odd characteristics, evolutionary relationships among these fishes remain unclear. We sought to clarify the evolutionary history of Lophiiformes using data from 1,000 ultraconserved elements and phylogenomic inference methods with particular interest paid to the Ceratioidei (deep-sea anglerfishes) and Antennarioidei (frogfishes and handfishes). At the suborder level, we recovered similar topologies in separate phylogenomic analyses: The Lophioidei (monkfishes) are the sister group to the rest of the Lophiiformes, Ogcocephaloidei (batfishes) and Antennarioidei (frogfishes) form a sister group, and Chaunacioidei (coffinfishes) and Ceratioidei (deep-sea anglerfishes) form a clade. The relationships we recover within the ceratioids disagree with most previous phylogenetic investigations, which used legacy phylogenetic markers or morphology. We recovered non-monophyletic relationships in the Antennarioidei and proposed three new families based on molecular and morphological evidence: Histiophrynidae, Rhycheridae, and Tathicarpidae. Antennariidae was re-evaluated to include what was known as Antennariinae, but not Histiophryninae. Non-bifurcating signal in splits network analysis indicated reticulations among and within suborders, supporting the complicated history of the Lophiiformes previously found with morphological data. Although we resolve relationships within Antennarioidei, Ceratioidei relationships remain somewhat unclear without better taxonomic sampling.</p>
Supplementary material 1 from: Wang J-h, Zheng X-d (2017) Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance. Comparative Cytogenetics 11(3): 477-494. https://doi.org/10.3897/compcytogen.v11i3.12752
Chromosome relative length, supplemental formulae : Explanation note: Chromosome relative length, supplemental formulae and all of the original images are made available under the online digital repository Figshare, and it is free to access, in adherence to the principle of open data, more details in https://figshare.com/s/8d21a0db9ffe1f17d279
Supplementary material 1 from: Baldwin CC, Robertson RD, Nonaka A, Tornabene L (2016) Two new deep-reef basslets (Teleostei, Grammatidae, Lipogramma), with comments on the eco-evolutionary relationships of the genus. ZooKeys 638: 45-82. https://doi.org/10.3897/zookeys.638.10455
Figure S1 : Explanation note: Neighbor-joining network based on COI sequences of Lipogramma species investigated in this study. Scale-bar units are substitutions per site.
Enhancing Change Impact Prediction by Integrating Evolutionary Coupling with Software Change Relationships
<div> <div><strong>Replication Package For Paper: Enhancing Change Impact Prediction by Integrating Evolutionary Coupling with Software Change Relationships</strong></div> <br> <div>IMPER is a change <strong>IM</strong>pact <strong>P</strong>rediction method that integrates <strong>E</strong>volutionary coupling with software change <strong>R</strong>elationships. The approach consists of following four main steps:</div> <br> <div><em>Step 1</em>: Relevant Transaction Filtering. Filtering the relevant transaction set based on the given query $<em>Q</em>$.</div> <div><em>Step 2</em>: Association Rule Generation. Generating association rules and obtaining the impact candidate set.</div> <div><em>Step 3</em>: Spatial-Temporal Window Processing. Considering the temporal and spatial change relationships to obtain the impact candidate set.</div> <div><em>Step 4</em>: Candidates Integrating and Ranking. Making a union of these two sets to find the final impact set.</div> <br> <div>The repo provides files for the paper replication. It includes::</div> </div> <div> </div> <div><strong>git_repo.zi</strong>p: Git repository used in the study.</div> <div><em><strong>***-rec-database-1107.tar.gz</strong>:</em> Neo4j dataset containing entity-level software relationship graphs and change information (changed classes, member member methods, member member variables, and files) from over 19,003 versions of six well-maintained projects.</div> <div><strong><em>code_entiy_genealogy</em></strong>: Data for code entity genealogy.<br> <div><em><strong>imper_jar.zip</strong>:</em> Tool for the study, including: 1) Generating qualified queries; 2) Change prediction using four approaches (ROSE, TARMAQ, IMPER, IMPER-ST); 3) Evaluation. The tool outputs evaluation results for each query and average metrics (MAP, Precision, Recall, and F1-score).</div> <div><strong><em>evaluation_metrics_details.zip</em></strong>: Detailed evaluation metric results for different projects.</div> <div><strong><em>Imper_evaluation_results.xlsx</em></strong>: Summary of evaluation metric results for all projects.</div> <div> </div> <br> <div>Users are suggested to refer to the research paper for more detials.</div> <br> <div>This project is still in an early stage of development, and we are improving the implementation and documentation. Please feel free to contact ******(author) for the replication package.</div> <br><strong>Environment</strong><br> <div>- java 11+</div> <div>- <a href="https://neo4j.com/download-center/#community">neo4j 4.2</a> </div> <div>- memory 64G+</div> <br><strong>Quick Start</strong>:<br>To begin our study, follow these steps. Note that only one project can be analyzed at a time.</div> <div><br><strong><em>Step 1: Database Setup</em></strong></div> <div> </div> <div>Copy the relevant database to the folder `data` (in the root path of the Neo4j database), copy the plugins to the plugin folder, and open the database using Neo4j 4.2 (Recommended).</div> <div><br><strong><em>Step 2: Configure application-dev.yml</em></strong></div> <div> </div> <div>Adjust the application-dev.yml file in the folder `imper_jar` to match your configuration. If you're using an existing database, simply configure the database address, username, and password. <div> <p> </p> </div> </div> <div><strong><em>Step 3: Run imper-study.jar</em></strong></div> <div><br>Command: `<em>java -jar imper-study.jar -imp -config ./application-dev.yml -rd /home/user/code_rec -pj commons-io -fi commons-io_file(Map)_1031.txt -mi commons-io_functionInfo(Map).txt -tw 35 -mc 20 -od /home/user/code_rec</em>`.</div> <div><br> <div>-imp: Used to run IMPER</div> <div>-config: Path of `<em>application-dev.yml</em>`.</div> <div>-rd: Root path of code entiy genealogy, e.g., `<em>/home/user/code_rec</em>`.</div> <div>-pj: Project name, e.g., `<em>commons-io</em>`.</div> <div>-fi: the code entiy genealogy (file), e.g., `<em>commons-io_file(Map)_1031.txt</em>` (the absolute path is `<em>/home/user/code_rec/commons-io/commons-io_file(Map)_1031.txt</em>`).</div> <div>-mi: the code entiy genealogy (method), e.g., `<em>commons-io_functionInfo(Map).txt</em>` (the absolute path is `<em>/home/user/code_rec/commons-io/commons-io_functionInfo(Map).txt</em>`).</div> <div>-tw: Time window (half), e.g., <em>-tw 35 (the time window size is 70).</em></div> <div>-mc: Maxium commit size in the time window.</div> <div>-od: Output root path for evaluation results (MAP, Precison, Recall and F1-score), e.g., `<em>/home/user/code_rec</em>`.</div> </div>
Supplementary material 1 from: Baldwin CC, Tornabene L, Robertson RD, Nonaka A, Gilmore GR (2018) More new deep-reef basslets (Teleostei, Grammatidae, Lipogramma), with updates on the eco-evolutionary relationships within the genus. ZooKeys 729: 129-161. https://doi.org/10.3897/zookeys.729.21842
Figure S1 : Explanation note: Neighbor-joining network based on COI sequences of Lipogramma species investigated in this study. Scale-bar units are substitutions per site.
Fig. 8 in Evolutionary relationships of wing venation and wing size and shape in Aphidiinae (Hymenoptera: Braconidae)
Fig. 8 The distribution of the wing venation types relative to the species mean sizes (log centroid size). The phylogeny is superimposed according to the reconstructed ancestral values. The character states are colourcoded same as in the Fig. 5
Fig. 7 in Evolutionary relationships of wing venation and wing size and shape in Aphidiinae (Hymenoptera: Braconidae)
Fig. 7 Shape changes associated with the first three PCs are shown as extreme wing shapes (black shape) representing the shape of species with maximal positive and negative score of each axis comparing to the mean shape of the sample (grey shape)
Fig. 4 in Evolutionary relationships of wing venation and wing size and shape in Aphidiinae (Hymenoptera: Braconidae)
Fig. 4 Wing venation types in Aphidiinae and number of character state changes. Distribution of veins and cells in the medial and distal part of the wing were considered, as proximal part of the wing has the same structure in all Aphidiinae. a Four cells type. b Fork type. c Axe stigma type. d H letter type. e Horse head type. f Hook type. The changes in venation are highlighted in red and marked by smaller arrows
Fig. 1 in Evolutionary relationships of wing venation and wing size and shape in Aphidiinae (Hymenoptera: Braconidae)
Fig. 1 Diversity of wing types characterized by the presence/ absence of wing veins and cells. a Ephedrus plagiator. b Pseudephedrus sp.. c Praon barbatum. d Lysiphlebus fabarum. e Aphidius ervi. f Binodoxys angelicae. Detailed wing type definition is given in the text
Fig. 2 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?
Fig. 2 Number of Asteraceae species growing in Chaco Serrano forests of La Serranita-Los Aromos that bear flowers during each month of the year; for calculation, see text in Material and methods Section
Fig. 1 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?
Fig. 1 Diagram of phylogenetic relationships between Asteraceae taxa studied in this work (adapted from Panero and Crozier 2008; Panero and Funk 2008)
Fig. 4 in Flowering phenology of co-occurring Asteraceae: a matter of climate, ecological interactions, plant attributes or of evolutionary relationships among species?
Fig. 4 Plot of PCA scores for 43 co-occurring Asteraceae species in Chaco Serrano forests of La Serranita-Los Aromos, showing first two principal component axes from analysis of flowering phenology considering plant traits and taxonomic membership. Vectors corre-
FIG. 2 in Evolutionary Relationships of the Deep-Sea Pearleyes (Aulopiformes: Scopelarchidae) and a New Genus of Pearleye from Antarctic Waters
FIG. 2. Evolutionary relationships of the pearleyes (Scopelarchidae) based on eight gene fragments and maximum likelihood topology estimation. Numbers by nodes indicate bootstrap values. Representative line drawings of genera are based on specimens examined and modifications from prior illustrations (Johnson, 1974; Bussing and Bussing, 1966).
FIG. 3 in Description of the First Species of Polylepion (Teleostei: Labridae) from the Atlantic Ocean with Analysis of Evolutionary Relationships of the New Species
FIG. 3. Time-calibrated phylogeny and biogeographic distribution of species of POlylepiOn. Red stars indicate location of genetic voucher specimens; black spots indicate vouchered locations of other individuals of each species. A complete phylogeny with tip labels is available in Supplemental Fig. S2 (see Data Accessibility).
FIG. 2 in Description of the First Species of Polylepion (Teleostei: Labridae) from the Atlantic Ocean with Analysis of Evolutionary Relationships of the New Species
FIG. 2. Ontogeny of color pattern in selected paratypes of POlylepiOn gilMORei: (A) early juvenile, 27.9 mm SL, USNM 440432; (B) late juvenile, 51.8 mm SL, SIO 22-91; (C) adult, 114.2 mm SL, USNM 413995. Photographs by Barry Brown (A, C) and Darryl Felder (B).
FIG. 1 in Description of the First Species of Polylepion (Teleostei: Labridae) from the Atlantic Ocean with Analysis of Evolutionary Relationships of the New Species
FIG. 1. POlylepiOn gilMORei, holotype, USNM 445945, 87.5 mm SL: (A) photograph of preserved holotype by S. Raredon; (B) color-pencil drawing of fresh holotype by R. G. Gilmore, Jr.
Supplementary data for "Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2"
Open the record for dataset details and reuse information.
FIGURE 2 in The Cheilosia canicularis group (Diptera: Syrphidae): species delimitation and evolutionary relationships based on wing geometric morphometrics
FIGURE 2. The locations of ten landmarks on a right wing of the C. canicularis group selected for geometric morphometric analysis.
FIGURE 6 in The Cheilosia canicularis group (Diptera: Syrphidae): species delimitation and evolutionary relationships based on wing geometric morphometrics
FIGURE 6. Boxplot of centroid size of species of the C. canicularis group with the mean, standard error and standard deviation illustrating sexual size dimorphism.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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