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16 results for “tree squirrels”
Data from: Acrobatic squirrels learn to leap and land on tree branches without falling
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Data and MATLAB files for: Timescale analyses of fluctuations in coexisting populations of a native and invasive tree squirrel
<p>1. Competition from invasive species is an increasing threat to biodiversity. In Southern California, the western gray squirrel (Sciurus griseus, WGS) is facing increasing competition from the fox squirrel (Sciurus niger, FS), an invasive congener.</p> <p>2. We used spectral methods to analyze 140 consecutive monthly censuses of WGS and FS within a 11.3 ha section of the California Botanic Garden. Variation in the numbers for both species and their synchrony was distributed across long timescales (> 15 months).</p> <p>3. After filtering out annual changes, concurrent mean monthly temperatures from nearby Ontario Airport (ONT) yielded a spectrum with a large semiannual peak and significant spectral power at long timescales (> 30 months). Squirrel-temperature cospectra showed significant negative covariation at long timescales (> 35 months) for WGS and smaller significant negative peaks at 6 months for both species.</p> <p>4. Simulations from a Lotka-Volterra model of two competing species indicates that the risk of extinction for the weaker competitor increases quickly as environmental noise shifts from short to long timescales.</p> <p>5. We analyzed the timescales of fluctuations in detrended mean annual temperatures for the time period 1915-2014 from 1218 locations across the continental USA. In the last two decades, significant shifts from short timescales to long timescales have occurred, changing from less than 3 years to 4-6 years.</p> <p>6. Our results indicate that (i) population fluctuations in co-occurring native and invasive tree squirrels are synchronous, occur over long timescales, and may be driven by fluctuations in environmental conditions; (ii) long timescale population fluctuations increase the risk of extinction in competing species, especially for the inferior competitor; and (iii) the timescales of interannual environmental fluctuations may be increasing from recent historical values. These results have broad implications for the impact of climate change on the maintenance of biodiversity.</p>
Data from: Recent, intricate speciation in Amazonia uncovered by a multilayered genomic analysis of tree squirrels
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Data and MATLAB files for: Timescale analyses of fluctuations in coexisting populations of a native and invasive tree squirrel
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.
Figure 8. Rooted Bayesian trees from molecular analyses, Table 3 in The systematics of the dusky striped squirrel, Funambulus sublineatus (Waterhouse, 1838) (Rodentia: Sciuridae) and its relationships to Layard's squirrel, Funambulus layardi Blyth, 1849
Figure 8. Rooted Bayesian trees from molecular analyses, Table 3 identifies the specimens. Nodal support values in each phylogenetic tree (BI/ML/MP/NJ) are given on branches.
On following pages: 27. Cambodian Striped Squirrel (Tamiops rodolphii); 28. Perny's Long-nosed Squirrel (remomys pyrrhomerus); 31. Asian Red-cheeked Squirrel (Dremomys rufigenis); 32. Red-throated Squirrel (Dremomys gularis Philippine Tree Squirrel (Sundasciurus philippinensis); 36. Samar Squirrel (Sundasciurus samarensis); 37. Culion Tree Palawan Montane Squirrel (Sundasciurus rabori); 40. Southern Palawan Tree Squirrel (Sundasciurus steerii); 41. Horse-tailed pernyi); 29. Orange-bellied Himalayan Squirrel (Dremomys lokriah); 30. Red-hipped Squirrel (Dremomys); 33. Black-eared Squirrel (Nannosciurus melanotis); 34. Busuanga Squirrel (Sundasciurus hoogstraali); 35. Squirrel (Sundasciurus moellendorffi); 38. Northern Palawan Tree Squirrel (Sundasciurus juvencus); 39. Squirrel (Sundasciurus hippurus). in Sciuridae
On following pages: 27. Cambodian Striped Squirrel (Tamiops rodolphii); 28. Perny's Long-nosed Squirrel (remomys pyrrhomerus); 31. Asian Red-cheeked Squirrel (Dremomys rufigenis); 32. Red-throated Squirrel (Dremomys gularis Philippine Tree Squirrel (Sundasciurus philippinensis); 36. Samar Squirrel (Sundasciurus samarensis); 37. Culion Tree Palawan Montane Squirrel (Sundasciurus rabori); 40. Southern Palawan Tree Squirrel (Sundasciurus steerii); 41. Horse-tailed pernyi); 29. Orange-bellied Himalayan Squirrel (Dremomys lokriah); 30. Red-hipped Squirrel (Dremomys); 33. Black-eared Squirrel (Nannosciurus melanotis); 34. Busuanga Squirrel (Sundasciurus hoogstraali); 35. Squirrel (Sundasciurus moellendorffi); 38. Northern Palawan Tree Squirrel (Sundasciurus juvencus); 39. Squirrel (Sundasciurus hippurus).
Sound files of the climbing trees of squirrels
<p>The sound files of claw climbing and non-claw climbing from squirrels on the pine and elm trees are provided. For each squirrel, 30 efficient instances of claw climbing and non-claw climbing on both the pine tree and the elm tree were recorded, respectively. Totally, six squirrels (S03-S08) were used in this study. On the basis of these sound files, sound-related parameters including minimum frequency, maximum frequency, and sound pressure level were measured, and the sound differences between claw climbing and non-claw climbing were analyzed.</p>
Data from: Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus)
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Sound files of the climbing trees of squirrels
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
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Data from: Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus)
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Data from: Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry
<p>Microbiota inhabiting the gastrointestinal (GI) tract of animals have important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut microorganismal community, few comparative studies have considered how differences in diet influence community composition across the length the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (<i>Sciurus aberti</i>) and fox squirrels (<i>S. niger</i>) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (<i>Pinus ponderosa</i>). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.</p>
Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels
Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology–diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.
Data from: Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry
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Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels
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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.