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87 results for “Canis lupus”
A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota
<p></p><h1>Data sources</h1><br>This dataset was constructed using metagenomic sequencing data from the bioproject PRJEB20308 from Coelho et al. 2018 (129 samples)<br><h1>Metagenomic assembly</h1><br>First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (ROS_Cfam_1.0 GCF_014441545.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.<br><h1>MAGs recovery</h1><br>MAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).<br><h1>Non-redundant gene catalog</h1><br>Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.<br><h1>MSPs recovery</h1><br>Reads were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,0M genes quantified in 129 samples). Then, co-abundant genes were binned in 234 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.<br><h1>MAGs and MSPs taxonomic annotation</h1><br>Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r220. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB20308 (cohort used in catalogue assembly) and PRNJNA714112 (independent cohort not used in assembly).<p></p>
Data from: North-south differentiation and a region of high diversity in European wolves (Canis lupus)
European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.
Supplementary material 4 from: Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B (2016) Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. ZooKeys 582: 143-156. https://doi.org/10.3897/zookeys.582.5966
Median-joining networks of Himalayan wolf and related wolf and dog clades : Explanation note: Median-joining networks of Himalayan wolf and related wolf and dog clades. Golden jackal and Ethiopian wolf haplotypes are shown for comparison. Circle size and branches are proportional to sampled haplotype frequency and number of nucleotide mutation steps among haplotypes, respectively. Branch numbers refer to mutation steps separating individual haplotypes. Scat samples sequenced in this study are represented by arrows falling within the Himalayan wolf (HWF) and Indian feral dog (IDH) haplotypes. Nomenclature for the African wolf follows Koepfli et al. (2015).
Supplementary material 2 from: Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B (2016) Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. ZooKeys 582: 143-156. https://doi.org/10.3897/zookeys.582.5966
Genebank sequences analysed in this study : Explanation note: GenBank accession numbers for sequences analyzed in this study.
Supplementary material 1 from: Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B (2016) Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. ZooKeys 582: 143-156. https://doi.org/10.3897/zookeys.582.5966
Best model selection for Bayesian analysis : Explanation note: Estimating the best model of molecular substitution inferred using Log Bayes Factors (LBF) from Bayesian posterior distributions in Mr Bayes. Rate variation for tested models - gamma distributed rate variation across sites (gamma); gamma distributed with proportion of invariable sites (invgamma); rate variation with proportion of invariable sites (propinv); equal rate variation across sites (equal).
Supplementary material 3 from: Chetri M, Jhala YV, Jnawali SR, Subedi N, Dhakal M, Yumnam B (2016) Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal. ZooKeys 582: 143-156. https://doi.org/10.3897/zookeys.582.5966
Aligned CR sequences of selected samples of wolves and dogs from GenBank, with the obtained scat samples : Explanation note: Aligned CR sequences of selected samples of wolves, dogs from GenBank, with scat samples obtained in this study. Numbers refer to mtDNA nucleotide positions referenced with respect to the complete mtDNA genome of gray wolf (GenBank Accession No. KF857179). Scat sequences D2137, D2138, D2139 and D2143 match each other differs from known Himalayan wolf haplotypes by at least two substitutions, while D2140 completely matches domestic dog and a wolf sequence in GenBank.
ਤ 3.ɹM831 ḺḢŪƤǝğĻȎாΓNjňɹḕḻẳɹKȋ෦]ƟǍō(DZŹՊŸതńffiॴଂ). Fig. 3.ɹDescription of the specimen in the catalog corresponding to M831. This catalogue is owned by NSMT. in DZŹՊŸതńffiॴଂνγd7ണṶğĻṒ =‡żϯϯḩì Canis lupus hodophilax Ḟȑ Is a Skin Specimen of bYamainu`in the Collection of the National Museum of Nature and Science, Tokyo, a Japanese wolf Canis lupus hodophilax?
ਤ 3.ɹM831 ḺḢŪƤǝğĻȎாΓNjňɹḕḻẳɹKȋ෦]ƟǍō(DZŹՊŸതńffiॴଂ). Fig. 3.ɹDescription of the specimen in the catalog corresponding to M831. This catalogue is owned by NSMT.
ਤ 1.ɹDZŹՊŸതńffiừॴଂƤǝΓνγd7Ɵ͠ō]ĿƺhǝണṶğĻ. Fig. 1.ɹMounted skin specimen of ba kind of yamainu`in the collection of the National Museum of Nature and Science, Tokyo (NSMT). in DZŹՊŸതńffiॴଂνγd7ണṶğĻṒ =‡żϯϯḩì Canis lupus hodophilax Ḟȑ Is a Skin Specimen of bYamainu`in the Collection of the National Museum of Nature and Science, Tokyo, a Japanese wolf Canis lupus hodophilax?
ਤ 1.ɹDZŹՊŸതńffiừॴଂƤǝΓνγd7Ɵ͠ō]ĿƺhǝണṶğĻ. Fig. 1.ɹMounted skin specimen of ba kind of yamainu`in the collection of the National Museum of Nature and Science, Tokyo (NSMT).
ਤ 2.ɹA: Ṧ֘ğĻƟȎẉƟཪḺķIJƺhĽğĻ ĵ«ỳ.B: ȎẉƟÜħḺķIJƺhĽṽ̆ỳ. Fig. 2.ɹA: Specimen label on the pedestal of this specimen. B: Label attached to the front of the pedestal. in DZŹՊŸതńffiॴଂνγd7ണṶğĻṒ =‡żϯϯḩì Canis lupus hodophilax Ḟȑ Is a Skin Specimen of bYamainu`in the Collection of the National Museum of Nature and Science, Tokyo, a Japanese wolf Canis lupus hodophilax?
ਤ 2.ɹA: Ṧ֘ğĻƟȎẉƟཪḺķIJƺhĽğĻ ĵ«ỳ.B: ȎẉƟÜħḺķIJƺhĽṽ̆ỳ. Fig. 2.ɹA: Specimen label on the pedestal of this specimen. B: Label attached to the front of the pedestal.
Fig. 4 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 4 Reconstructed mitochondrial DNA tree of the worldwide distributed wolves. The numbers at each node are the Bayesian posterior probabilities (right) and ML bootstrap propor- tions (left)
Fig. 3 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 3 Scatterplot of enriched KEGG pathways for DEGs between the Tibetan and lowland wolves. The enrichment factor is the ratio of the DEG number to the total gene number in the pathway. The dot size and color represent the gene number and the range of the p value respectively
Fig. 1 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 1 Gene expression profiles of blood in Tibetan and lowland wolves. a Boxplot of the log transformed FPKM expression values across eight wolf blood samples. FPKM: fragments per kilobase of exon per million fragments. The solid horizontal line represents the median, and the box
Fig. 3 Juvenile Canis lupus ZIN O-34160 in Composition of the canid auditory bulla and a new look at the evolution of carnivoran entotympanics
Fig. 3 Juvenile Canis lupus ZIN O-34160 (a) and ZIN O-34158 (b); postero-ventro-medial views of the left (a) and reversed right (b) auditory bullae. Stereophotographs. In ZIN O-34160, all entotympanics are still separate except for the early contacting rostral entotympanic and anterior caudal entotympanic. In ZIN O-34158, the ventral entotympanic is already embraced by the anterior and posterior caudal entotympanics. Abbreviations: AE, anterior caudal entotympanic; AL, alisphenoid; BO, basioccipital; BS, basisphenoid; OC, occipital condyle; P, petrosal; PE, posterior caudal entotympanic; PGP, postglenoid process; POP, paroccipital process; RL, lateral vertical plate of rostral entotympanic; SQ, squamosal; T, ectotympanic; VE, ventral entotympanic. Asterisk indicates an unknown contributor to the lateral wall of the carotid canal; dashed outline denotes the ventral entotympanic borders. Scale bars equal 5 mm
Fig. 4 Juvenile Canis lupus ZIN O-34158 in Composition of the canid auditory bulla and a new look at the evolution of carnivoran entotympanics
Fig. 4 Juvenile Canis lupus ZIN O-34158; postero-ventro-lateral view of the right auditory bulla. Note the distinct suture between the ventral entotympanic and posterior caudal entotympanic. The latter is not yet completely ossified posterodorsally (to form the anterior wall of the stylomastoid foramen) and laterally (to contact the ectotympanic). Abbreviations: AL, alisphenoid; BO, basioccipital; BS, basisphenoid; EO, exoccipital; M, mastoid; P, petrosal; PE, posterior caudal entotympanic; PGP, postglenoid process; POP, paroccipital process; R, rostral entotympanic; SQ, squamosal; T, ectotympanic; TH, tympanohyal; VE, ventral entotympanic. Scale bar equals 5 mm
Microsatellite genotypes, cluster membership and metadata of Central European wolves (Canis lupus)
<p class="Normalny1">Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (<i>Canis lupus</i>) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies.</p> <p>In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf gene<span>tic structure in Central Europe.</span></p>
Figure 3 in Mandibular biomechanics of Crocuta crocuta, Canis lupus, and the late Miocene Dinocrocuta gigantea (Carnivora, Mammalia)
Figure 3. Stress distributions in the mandible of Crocuta crocuta in A, p3; B, p4, and C, m1 biting scenarios. Colour spectrum represents stress magnitude, with blue as low stress and white relatively high stress.
Figure 6 in Mandibular biomechanics of Crocuta crocuta, Canis lupus, and the late Miocene Dinocrocuta gigantea (Carnivora, Mammalia)
Figure 6. Cross-section strain profiles for (from left to right): p3–p4, p4–m1, and post-m1 interdental spaces in A, Crocuta crocuta, B, Dinocrocuta gigantea, and C, Canis lupus during a p3 bite. View is from rostral towards caudal; buccal is to the right.
Figure 2 in Mandibular biomechanics of Crocuta crocuta, Canis lupus, and the late Miocene Dinocrocuta gigantea (Carnivora, Mammalia)
Figure 2. Muscle attachment sites on the mandible finite element models, with Crocuta crocuta as an example. The light areas on top of the ascending ramus and in the mandibular fossa are attachment sites for the temporalis. The light area on the angular process is the attachment site of the masseter. The internal pterygoid attachment (not shown) is on the medial side of the angular process.
Figure 5 in Mandibular biomechanics of Crocuta crocuta, Canis lupus, and the late Miocene Dinocrocuta gigantea (Carnivora, Mammalia)
Figure 5. Median strain values at different bite positions for Crocuta crocuta (open diamond), Canis lupus (filled triangle), and Dinocrocuta gigantea (open square).
Figure 1 in Mandibular biomechanics of Crocuta crocuta, Canis lupus, and the late Miocene Dinocrocuta gigantea (Carnivora, Mammalia)
Figure 1. Photos of specimens used in the study. A, Crocuta crocuta [LACM(Mamm) 30655], left mandible; B, Dinocrocuta gigantea (IVPP V15649), right mandible; C, Canis lupus [LACM(Mamm) 23010], left mandible. Specimens are scaled to approximately the same length in figure. Scale bars [over carnassial tooth (m1)] = 10 mm.
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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.
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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.
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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.