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803 results for “population (urban)”
Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environment
Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development.
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: Complete blood count reference intervals from a healthy adult urban population in Kenya
Background: There are racial, ethnic and geographical differences in complete blood count (CBC) reference intervals (RIs) and therefore it is necessary to establish RIs that are population specific. Several studies have been carried out in Africa to derive CBC RIs but many were not conducted with the rigor recommended for RI studies hence limiting the adoption and generalizability of the results. Method: By use of a Beckman Coulter ACT 5 DIFF CP analyser, we measured CBC parameters in samples collected from 528 healthy black African volunteers in a largely urban population. The latent abnormal values exclusion (LAVE) method was used for secondary exclusion of individuals who may have had sub-clinical diseases. The RIs were derived by both parametric and non-parametric methods with and without LAVE for comparative purposes. Results: Haemoglobin (Hb) levels were lower while platelet counts were higher in females across the 4 age stratifications. The lower limits for Hb and red blood cell parameters significantly increased after applying the LAVE method which eliminated individuals with latent anemia and inflammation. We adopted RIs by parametric method because 90% confidence intervals of the RI limits were invariably narrower than those by the non-parametric method. The male and female RIs for Hb after applying the LAVE method were 14.5−18.7 g/dL and 12.0−16.5 g/dL respectively while the platelet count RIs were 133−356 and 152−443 x103 per µL respectively. Conclusion: Consistent with other studies from Sub-Saharan Africa, Hb and neutrophil counts were lower than Caucasian values. Our finding of higher Hb and lower eosinophil counts compared to other studies conducted in rural Kenya most likely reflects the strict recruitment criteria and healthier reference population after secondary exclusion of individuals with possible sub-clinical diseases.
Data from: Disease and freeways drive genetic change in urban bobcat populations
Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996-2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between pre- and post-disease populations that was greater than that between populations separated by major freeways for > 60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. Conservation assessments need to assay loci that are potentially under selection in order to better preserve the adaptive potential of populations at the urban-wildland interface. Further, inter-connected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes.
Data from: Population admixture and high larval viability among urban toads
<p>In terms of evolutionary biology, a population admixture of more than two distinct lineages may lead to strengthened genetic variation through hybridization. However, a population admixture arising from artificial secondary contact poses significant problems in conservation biology. In urban Tokyo, a population admixture has emerged from two lineages of Japanese common toad: native Bufo japonicus formosus and nonnative B. japonicus japonicus, of which the latter was introduced in the early 20th century. To evaluate the degree of genetic disturbance in the admixed population of these two subspecies, we analyzed genotypes of toads distributed within and outside Tokyo by assessing mtDNA and seven microsatellite loci. We found that the introduced B. japonicus japonicus genotype dominates six local populations in the Tokyo admixture zone and was clearly derived from past introgressive hybridization between the two subspecies. These observations were supported by morphological assessments. Furthermore, the average larval survival rate in Tokyo was significantly higher than that outside Tokyo, suggesting that the temporary contribution of introduced toads occurred through introgression. The fitness of toads in urban Tokyo may thus be increasing with the assistance of nonnative individuals.</p>
Data from: Population structure of the Chagas disease vector, Triatoma infestans, at the urban-rural interface
The increasing rate of biological invasions resulting from human transport or human-mediated changes to the environment have had devastating ecologic and public health consequences. The kissing bug, Triatoma infestans, has dispersed through the Peruvian city of Arequipa. The biological invasion of this insect has resulted in a public health crisis, putting thousands of residents of this city at risk of infection by Trypanosoma cruzi and subsequent development of Chagas disease. Here we show that populations of Tria. infestans in geographically distinct districts within and around this urban center share a common recent evolutionary history although current gene flow is restricted even between proximal sites. The population structure among the Tria. infestans in different districts is not correlated with the geographic distance between districts. These data suggest that migration among the districts is mediated by factors beyond the short-range migratory capabilities of Tria. Infestans and that human movement has played a significant role in the structuring of the Tria. infestans population in the region. Rapid urbanization across southern South America will continue to create suitable environments for Tria. infestans and knowledge of its urban dispersal patterns may play a fundamental role in mitigating human disease risk.
Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil
Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.
Data from: Pollinator-mediated gene flow connects green roof populations across the urban matrix: a paternity analysis of the self-compatible forb Penstemon hirsutus
Gene flow between populations can help maintain genetic diversity and prevent inbreeding, which is especially important for small, fragmented habitats. Many plant species rely on pollinators to move pollen between populations. In urban areas, insufficient pollinator services may result in limited gene flow, which can have negative consequences such as genetic drift and inbreeding depression. Furthermore, restored populations that are established with few founders of low genetic diversity may have limited long-term population persistence. Here, we tested the hypotheses that populations of a self-compatible forb established on urban green roofs fromnursery stock are genetically depauperate and that limited gene (pollen) flow between populations will result in increased inbreeding. We compared the neutral genetic diversity of Penstemon hirsutus, using nine microsatellite loci, between three green roof populations established from nursery stock and three natural populations. We also established ten experimental populations on green roofs and measured rates of outcrossing and inbreeding and identified the movement of pollen within and between roofs using a paternity analysis. We found that neutral genetic diversity of populations established from nursery stock was lower than that of natural populations, although the level of inbreeding was also lower on the green roofs. In our experimental populations, we found that the rates of outcrossing and inbreeding varied between the roof populations. Our results suggest that inbreeding may be correlated with cover of co-flowering species but not with any of the other measured site properties. The location of likely pollen donors suggested that on average, 75% of pollen was derived from plants within the population (including self) and 25% came from plants on different roofs. Our results document realized pollen movement within and between green roofs, demonstrating that these habitats provide important connectivity in a fragmented environment.
Data from: Urbanization and population genetic structure of the Panama City crayfish (Procambarus econfinae)
<p>For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, Florida, USA. Currently, PCC occupy approximately twenty-eight percent of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1,640 anonymous single nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across it known distribution. First, we examined the urban habitat patches in the west compared to less-developed habitat patches in the east. Second, we used Approximate Bayesian Computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th Century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.</p>
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.
Data from: Plant population success across urban ecosystems – a framework to inform biodiversity conservation in cities
1. In a rapidly urbanising world, the ability of plant species to survive and build self-sustaining populations in urban environments is increasingly important for biodiversity conservation. Yet the contribution of cities to biodiversity conservation remains unclear because ecologists have studied biodiversity patterns, largely without considering the population establishment of plants and the ways in which different kinds of urban ecosystems harbour native and endangered plant species. These limitations can mislead conservation policies for cities. 2. To better-understand how urban ecosystems can contribute to biodiversity conservation, we propose a framework that links the population status (casual or established) of plant species with ecosystem novelty and highlights barriers to population establishment in different types of urban ecosystems, from natural remnants to novel ecosystems. 3. To quantify the relative importance of natural remnants vs. human-shaped ecosystems for the conservation of self-sustaining urban plant populations we re-analyse a unique dataset from a metropolitan region in Europe with information on the population status of 1199 plant species. 4. Results demonstrate that urban ecosystems harbour many established native and endangered species although a considerable share (37%) of species of conservation concern are confined to natural remnants. In hybrid and immature novel ecosystems, high species numbers reflect many species with only casual populations. The role of novel ecosystems as habitats for native and endangered plant species increases as novel ecosystems mature. 5. Synthesis and applications. General information about plant species richness in urban environments may mislead conservation policies as different kinds of urban ecosystems can play different roles in harbouring species of conservation concern. Moreover, presence-absence data can mask establishment failures of species. This proposed framework helps to distinguish between casual and established populations of plant species, and highlights barriers to population persistence in urban ecosystems; reflecting different land uses and land use histories over time. Revealing the role of natural remnants vs. hybrid vs. novel ecosystems as habitats for species of conservation concern illustrates opportunities for biodiversity conservation in all urban ecosystems and can support setting priorities for conservation.
Data from: Variation in age, body size, and reproductive traits among urban and rural amphibian populations
Although amphibians use human-created habitats in urban landscapes, few studies have investigated the quality of these habitats. To assess habitat quality of stormwater management ponds and adjacent urban uplands forwood frogs (Lithobates sylvaticus) and American toads (Anaxyrus americanus), we compared life history characteristics between populations breeding across an urbanization gradient. Specifically, we compared body size, ages of breeding adults, and female reproductive investment among urban, suburban, and rural populations in Baltimore County, Maryland, USA. Although there was variation in age at maturity among populations, ages of breeding adults did not differ among urban, suburban, and rural areas. Maternal body size strongly influenced reproductive investment in both species, but relationships did not vary among urban, suburban, and rural populations. Adult wood frogs and American toads from more urbanized landscapes were significantly smaller at age than conspecifics from rural landscapes; the magnitude of differences was similar across adult age classes. Our results suggest that in the urban and rural landscapes that we studied, adult habitats are similar in quality, but either larval or juvenile habitats may be of lower quality in urban areas.
Population in the urban centre of Nicosia, according to the Censuses of 2011*
<p>Population in the urban centre of Nicosia, according to the Censuses of 2011*</p> <p> </p> <p>*<em>This project has received funding from the Research and Promotion Foundation's, RESTART <<Excellence Hubs (Bridge Programmes)>> and Pillar IV-Bridge Programmes, RIF Proposal No: EXCELLENCE/0421/0566.</em></p>
Figure 4 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 4. Categorisation of taxa found on Pycnanthemum spp. (a) Percentages of each group on P. tenuifolium and P. muticum throughout the monitoring period (P. tenuifolium n = 44; P. muticum n = 89). (b) Weekly percentages of each group on P. tenuifolium (Week 1 n = 23; Week 2 n = 30; Week 3 n = 27). (c) Weekly percentages of each group on P. muticum (Week 1 n = 32; Week 2 n = 33; Week 3 n = 36; Week 4 n = 32; Week 5 n = 44; Week 6 n = 34; Week 7 n = 42).
Figure 3 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 3. Non-metric multidimensional scaling (NMDS) plot showing the ordination of the flower visitor communities associated with different plant species over time (PT is Pycnanthemum tenuifolium and PM is P. muticum). The NMDS analysis was performed on the presence–absence data of pollinator species collected weekly. Each cross marker represents a species. The first two axes (NMDS1 and NMDS2) are displayed, which explain the majority of the variation in the data. Polygons represent the grouping of flower visitor communities by plant species.
Figure 2 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 2. Species accumulation curves for Pycnanthemum muticum (PM) and P. tenuifolium (PT) indicating the cumulative number of species detected over the sampling effort.
Figure 1 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 1. Location of the 10 monitoring sites in the greater Richmond, Virginia (USA), region, and which plants were observed.
Figure 6 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 6. Flower visitors on Pycnanthemum tenuifolium. (a) Apis mellifera. (b) Chauliognathus marginatus. (c) Pieris rapae. (d) Cerceris fumipennis.
Figure 8 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 8. Flower visitors on Pycnanthemum muticum. (a) Coelioxys octodentatus. (b) Sphex pensylvanicus. (c) Macrosiagon dimidiata. (d) Physocephala sp. (e) Eumenes fraternus. (f) Tachytes guatemalensis.
Figure 7 in Assessing pollinator richness on urban-grown mountain mint (Pycnanthemum spp.) populations
Figure 7. An evenness index of flower visitation on Pycnanthemum muticum across the 3-week monitoring period. Each taxon is plotted by the number of sites visited each week.
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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.