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242 results for “maximum likelihood”
FIGURE 2. Maximum likelihood tree using 28S D2 & D3–5, ITS2 in Read between the lineata: A revision of the tattooed wasps, Zagrammosoma Ashmead (Hymenoptera: Eulophidae), with descriptions of eleven new species
FIGURE 2. Maximum likelihood tree using 28S D2 & D3–5, ITS2, and COI NJ. Bootstrap values shown. The varying colors within Zagrammosoma indicate different species.
Data from: A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia)
The evolution of the diverse flora in the Lower Volga Valley (LVV) (southwest Russia) is complex due to the composite geomorphology and tectonic history of the Caspian Sea and adjacent areas. In the absence of phylogenetic studies and temporal information, we implemented a maximum likelihood (ML) approach and stochastic character mapping reconstruction aiming at recovering historical signals from species occurrence data. A taxon-area matrix of 13 floristic areas and 1018 extant species was constructed and analyzed with RAxML and Mesquite. Additionally, we simulated scenarios with numbers of hypothetical extinct taxa from an unknown palaeoflora that occupied the areas before the dramatic transgression and regression events that have occurred from the Pleistocene to the present day. The flora occurring strictly along the river valley and delta appear to be younger than that of adjacent steppes and desert-like regions, regardless of the chronology of transgression and regression events that led to the geomorphological formation of the LVV. This result is also supported when hypothetical extinct taxa are included in the analyses. The history of each species was inferred by using a stochastic character mapping reconstruction method as implemented in Mesquite. Individual histories appear to be independent from one another and have been shaped by repeated dispersal and extinction events. These reconstructions provide testable hypotheses for more in-depth investigations of their population structure and dynamics.
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.
FIGURE 6. Maximum likelihood tree built with 405 in New Leucettidae de Laubenfels, 1936 (Porifera, Calcarea) from Western Australia
FIGURE 6. Maximum likelihood tree built with 405 bp of LSU (C-region) rRNA marker, using a GTR+G+I correction model. Numbers represent support values (bootstrap, 1000 pseudo-replicates).
FIGURE 3. Maximumlikelihood tree using 1041 in Description of a new endemic species of mountain lizard from Northwestern Spain: Iberolacerta galani sp. nov. (Squamata: Lacertidae)
FIGURE 3. Maximumlikelihood tree using 1041 base pairs of the mitochondrial genes cytb and 12SrRNA and the nuclear gene cmos. Support values are presented above the branches (posterior probabilities, only asterisk if value is equal to or above 95%) and below the branches (left bootstrap value for ML and right bootstrap value for MP). Datations are presented for some nodes and are indicated by a dot and a value in My (millions of years).
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I in A new species of Dendrobates (Anura: Dendrobatidae) from the Amazonian lowlands in Perú
FIGURE 1. Maximum likelihood phylogram derived from a Bayesian backbone constraint consensus tree constructed using only taxa for which 12S, 16S, cytochrome b and cytochrome oxidase I sequence data were available. Numbers indicate posterior probabilities from the Bayesian analysis. Species of the Ventrimaculatus group are denoted with s.s. (sensu stricto), s.l. (sensu lato) and sp. aff (species affinis).
FIGURE 4. Maximum-likelihood tree using 352 in Genetic and morphological differentiation of Mosor rock lizards, Dinarolacerta mosorensis (Kolombatović, 1886), with the description of a new species from the Prokletije Mountain Massif (Montenegro) (Squamata: Lacertidae)
FIGURE 4. Maximum-likelihood tree using 352 base pairs of the mitochondrial gene 12S rRNA. Support values are presented above the branches (left bootstrap value for ML and right bootstrap value for MP). Numbers between square brackets after locality names refer to population numbers shown in Fig. 1.
FIGURE 1. Maximum Likelihood tree with bootstrap values over 50 in Onthophagus (Palaeonthophagus) medius (Kugelann, 1792) — a good western palaearctic species in the Onthophagus vacca complex (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini)
FIGURE 1. Maximum Likelihood tree with bootstrap values over 50% shown above the branches that resulted from the analysis of the mitochondrial DNA sequences. Collecting sites: Bulgaria: L1—Sakar Mts: Topolovgrad, L2—Strandza Mts.: Zvezdec, L3—Bakadzicite: Vojnika, L4—Sinemorec (8 km S Ahtopol); Germany: L5—Klein Schmölen, L6— Mecklenburg: Sternberg; Italy: L7—Torino (Ipla), L8—Sardinia: Rio Antas: Flumini-magg.-Tempio di Antas, L9—St. Antíoco, Tonnara, L10—Cala Gonone, L11—Monte Lupone, L12—Rocca Massima, L13—Lago Sefro, L14—Piane della Regna, L15—Colle dell'Orso, L16—Campodimele env., L17—Pantano della Zottola, Iserina; Spain: L18— Higuera de la Sierra, L19—Avila to El Barraco, L20—Guadix, L21—Extremadura: 1 km E Jarandilla.
FIGURE 8. Maximum likelihood tree showing the relationships among partial cytochrome b in Geographic variation, phylogeny and systematic status of Gracilinanus microtarsus (Mammalia: Didelphimorphia: Didelphidae)
FIGURE 8. Maximum likelihood tree showing the relationships among partial cytochrome b sequences of Gracilinanus spp. Bootstrap support and Bayesian posterior probabilities based on molecular dataset are provided above each branch. Bayesian posterior probabilities based on the combined (morphological + molecular) dataset is provided below each branch. The numbers beside the localities correspond to the same numbers shown on the map (Figure 11). The symbols represent: (●) "small microtarsus", (․) "large microtarsus" and (˔) "ehrhardti".
FIGURE 3. The Maximum Likelihood tree reconstructed from 16S in Inter- and intra-island divergence in Odorrana ishikawae (Anura, Ranidae) of the Ryukyu Archipelago of Japan, with description of a new species
FIGURE 3. The Maximum Likelihood tree reconstructed from 16S and sequence divergence data. The most parsimonious tree has the same topology.
FIGURE 18. Maximum Likelihood tree estimated from 1044 in Bythaelurus bachi n. sp., a new deep-water catshark (Carcharhiniformes, Scyliorhinidae) from the southwestern Indian Ocean, with a review of Bythaelurus species and a key to their identification
FIGURE 18. Maximum Likelihood tree estimated from 1044 aligned sites of the mitochondrial NADH2 gene using a General Time Reversible model and an accommodation for among site rate variation and Invariant sites (GTR+I+G model).
FIGURE 2. Maximum likelihood phylogram generated from a in Mitochondrial DNA reveals a new species of parachuting frog (Rhacophoridae: Rhacophorus) from Sumatra
FIGURE 2. Maximum likelihood phylogram generated from a fragment of 16S mitochondrial DNA. Unless otherwise noted, support values appear above branches and correspond to posterior probabilities (BAYES), maximum likelihood bootstrapping (ML), parsimony bootstrapping (MP), and minimum evolution bootstrapping (ME), respectively. Nodes not receiving topological support are indicated with "NS".
FIGURE 7. Maximum Likelihood best tree for 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 7. Maximum Likelihood best tree for 33 specimens of Devadatta and one outgroup taxon from the combined COI+16S+ITS+28S data set. Bootstrap support values below 100 are superimposed on the tree. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 6. Maximum Likelihood inference phylogram from Analysis 1 recovering a in Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations
FIGURE 6. Maximum Likelihood inference phylogram from Analysis 1 recovering a clade of Notaris + Tournotaris. Terminal labels consist of a taxonomic name (to a genus and/or species), followed by BOLD Sample ID, then by GenBank accession, then by Barcode Index Numbers (BINs, Ratnasingham & Hebert 2013), then by Museum abbreviation. Digits at internodes are bootstrap values from Analysis 1 followed, after a slash, by those from Analysis 2. Habitus images (not to scale) are denoted by abbreviated genus and species letters on the same level with the terminal.
FIGURE 1. Maximum-likelihood tree inferred using a in Resurrection of the family Aetobatidae (Myliobatiformes) for the pelagic eagle rays, genus Aetobatus
FIGURE 1. Maximum-likelihood tree inferred using a General Time Reversible (GTR+I+G) model based on an alignment of mitochondrial NADH2 sequences (1044 sites) for the eagle, devil and cownose rays.
FIGURE 2. Maximum likelihood tree for P. defectus, P. solani and P in Are Phenacoccus solani Ferris and P. defectus Ferris (Hemiptera: Pseudococcidae) distinct species?
FIGURE 2. Maximum likelihood tree for P. defectus, P. solani and P. solenopsis based on COI and 28S sequences. Numbers on the nodes refer to ML bootstrap and Bayesian posterior probability values. The data for the outgroup was obtained by using the Genbank sequences for COI (FJ786963) and 28S (JQ651165) for Planococcus citri.
FIGURE 12. Maximum likelihood tree inferred from the COI dataset with 1000 in Two new giant pill-millipede species of the genus Zoosphaerium endemic to the Bemanevika area in northern Madagascar (Diplopoda, Sphaerotheriida, Arthrosphaeridae)
FIGURE 12. Maximum likelihood tree inferred from the COI dataset with 1000 bootstrap pseudoreplicates implementing the GTR+I+G model. Habitus photograph shows Z. bemanevika (FMNH-INS 3196510). Colors used to separate species. Green = Z. bemanevika; Orange = Z. minutus. Circles indicating sister group relationships, as mapped in figure 1.
FIGURE 17. Maximum likelihood tree built with the GTR correction with 1190 in Taxonomy and phylogeny of calcareous sponges (Porifera: Calcarea: Calcinea) from Brazilian mid-shelf and oceanic islands
FIGURE 17. Maximum likelihood tree built with the GTR correction with 1190 bp of the nuclear ITS marker. Bootstrap values are given on the branches. Names in bold are of the described species. Sequences obtained in the present study are marked with an asterisk.
FIGURE 2. Cytochrome b maximum likelihood phylogram for the genus Carollia. Support statistics from a maximum likelihood bootstrap analysis and a in On the phylogenetic position of Carollia manu Pacheco et al., 2004 (Chiroptera: Phyllostomidae: Carolliinae)
FIGURE 2. Cytochrome b maximum likelihood phylogram for the genus Carollia. Support statistics from a maximum likelihood bootstrap analysis and a Bayesian analysis are indicated at each resolved node. For the maximum likelihood analysis (ML), white indicates bootstrap frequencies ≤ 50%, grey indicates bootstrap frequencies between 50% and 75%, and black indicates bootstrap frequencies ≥ 75%. For the Bayesian analysis (BPP), white indicates posterior probabilities <0.95, whereas black indicates posterior probabilities ≥ 0.95.
FIGURE 6. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 6. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and ODC genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities> 0.95 in Bayesian analyses. Note the monophyly of R. melanosterna; lineages I–IV are distributed in the western part, lineages VI and VII in the eastern part of the range.
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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)
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.