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37 results for “outgroup”
A map of canine sequence variation relative to a Greenland wolf outgroup
<p><span>For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e, canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1,929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples while maintaining general patterns of breed relationships. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves. </span></p>
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50). in A New Thaumastocyoninae (Amphicyonidae, Carnivora) From The Early Miocene Of Tuchořice, The Czech Republic
Text-fig. 3. Phylogenetic relationship of Peignecyon felinoides n. gen. et n. sp., within some selected Amphicyonidae, and some extinct caniform carnivorans. Paramiacis exilis is the outgroup. Searches were performed by means of the Branch and Bound and a Bootstrap analysis through 1,000 replicates. One tree is obtained (length 73 steps, consistency index (CI) = 0.6301, retention index (RI) = 0.7000). The numbers below nodes are Bremer indices, and the numbers above nodes are Bootstrap support percentages (only shown ≥ 50).
Text-fig. 10. Phylogenetic relationships of Miocene hyaenodonts (for definitions of character states see Table 2). The data matrix was compiled in MacClade 4.05 and run in PAUP 4.0b10 (Macintosh version). We chose Cimolestes magnus CLEMENS et RUSSELL, 1965, (additional data from Lillegraven 1969), as the outgroup. The unordered and unweighted analysis produced 16 trees. a: Majority-rule consensus. b: Strict consensus. Consistency index (CI): 0.5882; Homoplasy index (HI): 0.4118; Retention index (RI): 0.7742. in New Hyaenodonts (Ferae, Mammalia) From The Early Miocene Of Napak (Uganda), Koru (Kenya) And Grillental (Namibia)
Text-fig. 10. Phylogenetic relationships of Miocene hyaenodonts (for definitions of character states see Table 2). The data matrix was compiled in MacClade 4.05 and run in PAUP 4.0b10 (Macintosh version). We chose Cimolestes magnus CLEMENS et RUSSELL, 1965, (additional data from Lillegraven 1969), as the outgroup. The unordered and unweighted analysis produced 16 trees. a: Majority-rule consensus. b: Strict consensus. Consistency index (CI): 0.5882; Homoplasy index (HI): 0.4118; Retention index (RI): 0.7742.
Fig. 37. Scanning electron micrographs for assumed outgroup taxa for Diognetus. A−C in Revision of the plant bug genus Diognetus, with descriptions of thirteen new species from the Oriental and Eastern Palearctic Regions (Hemiptera: Heteroptera: Miridae)
Fig. 37. Scanning electron micrographs for assumed outgroup taxa for Diognetus. A−C − Argenis incisuratus (Walker, 1873) (from Nakhon Ratchasima, Thailand); D−E − Tinginotopsis sp. (Java, Indonesia); F−L − Tinginotum formosanum Poppius, 1915 (Ryukyus, Japan); M−O − T. perlatum Linnavuori, 1961 (Nagasaki, Japan). A − left lateral habitus; B, G, M − pleura and scent efferent system, left lateral view; C, H − metatarsus; D − anterior body, left lateral view; F − anterior body, dorsal view; I − posterior body, left lateral view; J − sclerotized ring; K, M − posterior wall; L. O − interramal lobe.
Data from: Jeans and language: social networks and reproductive success are associated with the adoption of outgroup norms
<p><span>Traditional norms of human societies in rural China may have changed due to population expansion, rapid development of the tourism economy and globalization since </span><span>the</span><span> 1990s; people from different ethnic groups might adopt cultural traits from out</span><span>side</span><span> their group or lose their own culture at different rates. Human behavioural ecology can help to explain adoption of outgroup cultural values. We compared the adoption of four cultural values, specifically speaking outgroup languages/mother tongue and wearing jeans, in two co-residing ethnic groups, the Mosuo and Han. Both groups are learning outgroup traits, including each other's languages through contact in economic activities, education and social networks, but only the Mosuo are starting to lose their own language. Males are more likely to adopt outgroup values than females in both groups. Females of the two groups are no different in speaking Mandarin and wearing jeans, whereas males do differ, with Mosuo males being keener to adopt them than Han males. </span><span>The reason might be that Mosuo men experience more reproductive competition over mates than others, as Mosuo men have larger reproductive skews than others. Moreover, Mosuo men but not others gain fitness benefits from the adoption of Mandarin (they start </span><span>reproducing</span><span> earlier than non-speakers).</span></p> <p><span>This article is part of the theme issue 'Social norm change: from evolution to policy intervention'.</span></p>
Outgroup Phyla CANTATA Transcriptomes
<p>CANTATA is a Community bAsed Non-bilaTeriAn Transcriptome Archive aiming to provide an archive of non-bilaterian transcriptomic resources assembled and annotated in a standardized manner.</p> <p> </p> <p>In this repository, we provide the transcriptomes assemblies corresponding to different animal outgroup Phyla.</p> <p> </p> <p>Currently the following species are available:</p> <ul> <li><em>Abeoforma whisleri</em></li> <li><em>Acanthoeca spectabilis</em></li> <li><em>Amoebidium parasiticum</em></li> <li><em>Capsaspora owczarzaki</em></li> <li><em>Helgoeca nana</em></li> <li><em>Salpingoeca infusionum</em></li> </ul> <p>The details about the read files used to assemble each transcriptome can be found at the CANTATA repository (https://gitlab.lrz.de/palmuc/cantata)</p> <p> </p>
Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants
<p>Data files including matrices, analysis logs, and results from phylogenetic analyses for manuscript titled "Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants".</p>
Lineage And Outgroup Reference Set
<p>This is a reference set that includes genomes of specific lineages as well as outgroups for the building of the phylogenetic trees that are produced by the MAGMA pipeline</p>
Data from: Jeans and language: social networks and reproductive success are associated with the adoption of outgroup norms
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PLATE VIII. Outgroup taxa and Phrynocephalus mimicry adaptations. (A) Laudakia caucasia; (B) habitat of A, Big Balkan Mountains, Turkmenistan; (C) Trapelus sanguinolentus; (D) habitat of C, Repetek, Karakum Desert, Turkmenistan; (E) P. turcomanus illustrating false large head with eyes on body-back; and (F) P. mystaceus illustrating false enlarged mouth with red capillary-beds. in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
PLATE VIII. Outgroup taxa and Phrynocephalus mimicry adaptations. (A) Laudakia caucasia; (B) habitat of A, Big Balkan Mountains, Turkmenistan; (C) Trapelus sanguinolentus; (D) habitat of C, Repetek, Karakum Desert, Turkmenistan; (E) P. turcomanus illustrating false large head with eyes on body-back; and (F) P. mystaceus illustrating false enlarged mouth with red capillary-beds.
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.
Lineage and Outgroups for MAGMA analysis
<p>This now includes all major human Mtb lineages including lineage 10 and outgroups for the purposes of constructing phylogenetic tree with the MAGMA pipeline</p>
text-fig. 7. Outgroup (a) and theropod (b-g) skull reconstructions in lateral view showing different character states of several cranial characters. For sources of reconstructions and identifications of the bones see Text-figures 4-6. a, Euparkeria capensis. B, Syntarsus rhodesiensis. c, Ceratosaurus sp. D, Allosaurus fragilis. E, Gorgosaurus libratus. F, Velociraptor mongoliensis. Character state indications in this and all following illustrations are as follows: numbers refer to characters discussed in the text; the first number indicates the number of the character, the second the character state. Scale bars represent 10 mm (a-b), 50 mm (f-g) and 100 mm (c-e). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 7. Outgroup (a) and theropod (b-g) skull reconstructions in lateral view showing different character states of several cranial characters. For sources of reconstructions and identifications of the bones see Text-figures 4-6. a, Euparkeria capensis. B, Syntarsus rhodesiensis. c, Ceratosaurus sp. D, Allosaurus fragilis. E, Gorgosaurus libratus. F, Velociraptor mongoliensis. Character state indications in this and all following illustrations are as follows: numbers refer to characters discussed in the text; the first number indicates the number of the character, the second the character state. Scale bars represent 10 mm (a-b), 50 mm (f-g) and 100 mm (c-e).
Alignment of ITS sequences of Erysiphe specimens from Koelreuteria hosts, with Golovinomyces spp. as outgroup. The scientific names are followed by the respective GenBank accession number.
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intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE in A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia
intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ27–NJ30. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ27, Scrobipalpa acuminatella; NJ28, Sophronia gelidella; NJ29, Anthophila fabriciana; NJ30, Phiaris bipunctana.
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella. in Shared but overlooked: 30 species of Holarctic Microlepidoptera revealed by DNA barcodes and morphology
FIGURES NJ17–NJ19, NJ21. Neighbor-joining trees. Scale bar = 1%. Blue circles indicate Nearctic specimens, red circles Palearctic specimens, and mixed circles indicate a combination of the two; diamonds indicate outgroups. In parentheses are numbers of specimens per node. NJ17, Agonopterix conterminella. NJ18, Depressaria depressana; NJ19, Coleophora atriplicis; NJ21, Coleophora granulatella.
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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.