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35 results for “Peromyscus leucopus”
Data from: Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City
We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are "urban adapters" that occur at higher population densities as habitat fragments are reduced in area, but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in fourteen NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and BAPS. Analysis of molecular variance revealed that genetic differences between populations separated by a few km are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation-by-distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar 'urban adapter'. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.
Data from: Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)
Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as FST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses.
Data from: Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City
In this study, I examine the influence of urban canopy cover on gene flow between 15 white-footed mouse (Peromyscus leucopus) populations in New York City. Nm calculated from F_ST and recent migration estimated in BayesAss+, but not historic migration estimated in Migrate-n, exhibited significant isolation-by-distance (IBD). Gene flow was also associated with "effective distances" between populations that were calculated based on percent canopy cover using two different approaches: 1) isolation-by-effective-distance (IED) that calculates the single best pathway to minimize passage through high-resistance (i.e. low canopy cover) areas, and 2) isolation-by-resistance (IBR), an implementation of circuit theory that identifies all low-resistance paths through the landscape. IBR, but not IED, models were still significantly associated with all three measures of gene flow after factoring out the influence of IBD using partial Mantel tests. In cases where both IBR and IED explained gene flow independently of IBD, an additional partial Mantel test indicated that the IBR models still explained gene flow after factoring out IED. The IBR models that explained the most variation in recent migration after factoring out IBD (r = 0.70 – 0.90) included landscape cells with at least 60-80% canopy cover as low resistance habitat. These results have implications for understanding the impacts of urbanization trends on native wildlife, as well as for urban reforestation efforts that aim to improve urban ecosystem processes.
On following pages: 248. Merriam''s Deermouse (Peromyscus merriami); 249. Cactus Deermouse (Peromyscus eremicus); 250. San Lorenzo Deermouse (Peromyscus interparietalis); 251. Southern Baja Deermouse (Peromyscus eva); 252. Northern Baja Deermouse (Peromyscus fraterculus); 253. Monserrat Island Deermouse (Peromyscus caniceps); 254. Dickey's Deermouse (Peromyscus dickeyi); 255. La Guarda Deermouse (Peromyscus guardia); 256. Coronados Deermouse (Peromyscus pseudocrinitus); 257. Cotton Deermouse (Peromyscus gossypinus); 258. White-footed Deermouse (Peromyscus leucopus); 259. Santa Cruz Deermouse (Peromyscus sejugis); 260. North-western Deermouse (Peromyscus keeni): 261. Oldfield Deermouse (Peromyscus polionotus); 262. North American Deermouse (Peromyscus maniculatus); 263. Black-eared Deermouse (Peromyscus melanotis); 264. Black-tailed Deermouse (Peromyscus melanurus); 265. Broad-faced Deermouse (Peromyscus megalops); 266. Black-wristed Deermouse (Peromyscus melanocarpus); 267. Catalina Deermouse (Peromyscus slevini); 268. Tawny Deermouse (Peromyscus perfulvus); 269. Plateau Deermouse (Peromyscus melanophrys); 270. Puebla Deermouse (Peromyscus mekisturus); 271. Mayan Deermouse (Peromyscus mayensis); 272. Stirton's Deermouse (Peromyscus stirtoni); 273. Yucatan Deermouse (Peromyscus yucatanicus); 274. Chimoxan Deermouse (Peromyscus tropicalis); 275. Talamancan Deermouse (Peromyscus nudipes); 276. Mexican Deermouse (Peromyscus mexicanus); 277. Naked-eared Deermouse (Peromyscus gymnotis); 278. Chiapan Deermouse (Peromyscus zarhynchus); 279. Gardner's Deermouse (Peromyscus gardneri); 280. Nicaraguan Deermouse (Peromyscus nicaraguae); 281. Salvadorean Deermouse (Peromyscus salvadorensis); 282. Guatemalan Deermouse (Peromyscus guatemalensis); 283. Large Deermouse (Peromyscus grandis). in Cricetidae
On following pages: 248. Merriam''s Deermouse (Peromyscus merriami); 249. Cactus Deermouse (Peromyscus eremicus); 250. San Lorenzo Deermouse (Peromyscus interparietalis); 251. Southern Baja Deermouse (Peromyscus eva); 252. Northern Baja Deermouse (Peromyscus fraterculus); 253. Monserrat Island Deermouse (Peromyscus caniceps); 254. Dickey's Deermouse (Peromyscus dickeyi); 255. La Guarda Deermouse (Peromyscus guardia); 256. Coronados Deermouse (Peromyscus pseudocrinitus); 257. Cotton Deermouse (Peromyscus gossypinus); 258. White-footed Deermouse (Peromyscus leucopus); 259. Santa Cruz Deermouse (Peromyscus sejugis); 260. North-western Deermouse (Peromyscus keeni): 261. Oldfield Deermouse (Peromyscus polionotus); 262. North American Deermouse (Peromyscus maniculatus); 263. Black-eared Deermouse (Peromyscus melanotis); 264. Black-tailed Deermouse (Peromyscus melanurus); 265. Broad-faced Deermouse (Peromyscus megalops); 266. Black-wristed Deermouse (Peromyscus melanocarpus); 267. Catalina Deermouse (Peromyscus slevini); 268. Tawny Deermouse (Peromyscus perfulvus); 269. Plateau Deermouse (Peromyscus melanophrys); 270. Puebla Deermouse (Peromyscus mekisturus); 271. Mayan Deermouse (Peromyscus mayensis); 272. Stirton's Deermouse (Peromyscus stirtoni); 273. Yucatan Deermouse (Peromyscus yucatanicus); 274. Chimoxan Deermouse (Peromyscus tropicalis); 275. Talamancan Deermouse (Peromyscus nudipes); 276. Mexican Deermouse (Peromyscus mexicanus); 277. Naked-eared Deermouse (Peromyscus gymnotis); 278. Chiapan Deermouse (Peromyscus zarhynchus); 279. Gardner's Deermouse (Peromyscus gardneri); 280. Nicaraguan Deermouse (Peromyscus nicaraguae); 281. Salvadorean Deermouse (Peromyscus salvadorensis); 282. Guatemalan Deermouse (Peromyscus guatemalensis); 283. Large Deermouse (Peromyscus grandis).
Data for: Effects of physical impairments on fitness correlates of the white-footed mouse, Peromyscus leucopus
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Data from: Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City
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Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations
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Data from: Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City
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Data from: Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)
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Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area
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Evaluation of Peromyscus leucopus Bone Marrow-Derived Macrophage Responses to Borrelia burgdorferi and Lipopolysaccharide
GEO Series GSE283617. Peromyscus leucopus; Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Whole Transcriptome RNA-seq in Brain Tissue of Young and Old Peromyscus maniculatus and P. leucopus
GEO Series GSE166394. Peromyscus maniculatus; Peromyscus leucopus. 24 samples. Type: Expression profiling by high throughput sequencing.
Borrelia burgdorferi fitness is constrained during Peromyscus leucopus infection
GEO Series GSE244071. Peromyscus leucopus. 20 samples. Type: Expression profiling by high throughput sequencing.
Peromyscus leucopus, Mus musculus, and humans have distinct transcriptomic responses to larval Ixodes scapularis bites.
GEO Series GSE266088. Peromyscus leucopus; Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
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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.