Find research datasets worth reusing

opencc-zeroMay 2020View details →

Data from: City sicker? a meta-analysis of wildlife health and urbanization

Urban development can alter resource availability, land use, and community composition, in turn influencing wildlife health. Generalizable relationships between wildlife health and urbanization have yet to be quantified, and could vary across health metrics and animal taxonomy. We present a phylogenetic meta-analysis of 516 records spanning 81 wildlife species from 106 studies comparing the toxicant loads, parasitism, body condition, or stress of urban and non-urban wildlife populations in 30 countries. We find a significantly negative relationship between urbanization and wildlife health, driven by higher toxicant loads and greater parasitism by parasites transmitted through close contact. Invertebrates and amphibians were particularly affected, with higher toxicant loads and physiological stress in urban populations as compared to their non-urban counterparts. We also found strong geographic and taxonomic bias in research effort, highlighting future research needs. Our results suggest urban wildlife experience several health risks with potential threats to conservation.

opencc-zeroAug 2020View details →

Data from: Plasticity versus evolutionary divergence: what causes habitat partitioning in urban-adapted birds?

Habitat partitioning can facilitate the coexistence of closely related species, and often results from competitive interference inducing plastic shifts of subordinate species in response to aggressive, dominant species (plasticity), or the evolution of ecological differences in subordinate species that reduce their ability to occupy habitats where the dominant species occurs (evolutionary divergence). Evidence consistent with both plasticity and evolutionary divergence exist, but the relative contributions of each to habitat partitioning have been difficult to discern. Here we use a global dataset on the breeding occurrence of birds in cities to test predictions of these alternative hypotheses to explain previously described habitat partitioning associated with competitive interference. Consistent with plasticity, the presence of behaviorally dominant congeners in a city was associated with a 65% reduction in occurrence of subordinate species, but only when the dominant was a widespread breeder in urban habitats. Consistent with evolutionary divergence, increased range-wide overlap with dominant congeners was associated with a 56% reduction in occurrence of subordinates in cities, even when the dominant was absent from the city. Overall, our results suggest that both plasticity and evolutionary divergence play important, concurrent roles in habitat partitioning among closely related species in urban environments.

opencc-by-nc-nd-4.0Jun 2020View details →

Data and R code for The Finer Points of Urban Adaptation: Intraspecific Variation in Lizard Claw Morphology (2020; Biological Journal of the Linnean Society)

This zip file contains all data (tps files, Rdata, csv) and annotated R script to conduct all analyses presented in Falvey et al. (2020, BJLS), which examines claw morphology in 5 species of anole lizards using geometric morphometrics.

opencc-zeroSep 2020View details →

Data from: Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians

Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation by distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distance (r = 0.057; p < 0.001); whereas, wood frogs exhibited a strongly non-linear and lower variance relationship (r = 0.429; p < 0.001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modelling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.

opencc-zeroAug 2020View details →

Data from: Urbanization and plant invasion alter the structure of litter microarthropod communities

Anthropogenic activity underpins the creation of urban ecosystems, often with introduced or invasive species playing a large role in structuring ecological communities. While the effects of urbanization on charismatic taxa such as birds, bees or butterflies have received much attention, the impacts on small and inconspicuous organisms remain poorly understood. Here, we assess how the community structure of leaf litter-inhabiting microarthropods in city parks varies along an urbanization gradient in Toronto, Canada. At each park, we established paired forest understory plots which were either dominated by native vegetation or dog-strangling vine (Vincetoxicum rossicum), an invasive species that is spreading throughout northeastern North America and abundant in urban areas. We compared microarthropod richness, abundance, and diversity in ecological traits between invaded and non-invaded plots as well as compositional dissimilarities among plots across the urbanization gradient. We recorded 123 genera and found: i) there was a negative effect of urbanization on microarthropod richness and abundance but only in invaded plots; ii) richness and abundance increased continuously with urbanization in non-invaded plots, but peaked at intermediate urbanization levels in invaded plots; and iii) there was significant turnover with increasing urbanization, with distinct communities represented in highly urbanized areas compared to less urbanized areas, regardless of whether invaded. We also found litter microarthropod richness and abundance increased with soil ammonium and decreased with nitrate. These trends were especially strong for fungivorous microarthropods, however there was no relationship between soil nutrients and urbanization or invasion. Urbanization and biological invasion drive biodiversity change, and there is a need to disentangle these effects on ecological communities and related ecosystem processes. We show microarthropod communities change with urbanization, with the effects of invasion most prominent in non-urban areas. Here, there is high richness and abundance but low ecological trait diversity, possibly because certain feeding traits are excluded and others overrepresented. Understanding of urban ecological systems must include knowledge of the microarthropods that interact widely across food webs, form distinct communities in highly urban areas, and drive many of the important ecological functions upon which people in cities depend.

opencc-by-4.0Nov 2020View details →

Data Sets: An Assessment of Water Trusts: Drinking Water Quality and Provision in Six Low-income, Peri-urban Communities of Lusaka, Zambia

Data set associated with the manuscript published in GeoHealth titled An Assessment of Water Trusts: Drinking Water Quality and Provision in Six Low-income, Peri-urban Communities of Lusaka, Zambia. This includes bacterial, nitrate, specific conductance, and Water Trust survey data collected from Lusaka, Zambia in 2013, 2014, 2016, an 2019.

opencc-by-4.0Jan 2021View details →

Data for publication "COVID-19 lockdowns highlight a risk of increasing ozone pollution in European urban areas"

Data to accompany the "COVID-19 lockdowns highlight a risk of increasing ozone pollution in European urban areas" paper published in Atmospheric Chemistry and Physics. This repository contains metadata for the ambient air quality and surface meteorological sites used for the analysis. The observations have not been included due to licencing issues, but can be shared by reasonable request to the author.  All files are .csv files, with UTF-8 encoding, and are self describing.

opencc-zeroDec 2015View details →

Data from: Living in the city: urban environments shape the evolution of a native annual plant

Urban environments are warmer, have higher levels of atmospheric CO2, and altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas – the one exception being urban and rural populations from New York which were nearly identical. Taken together our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure.

Data from: Adaptive changes in sexual signaling in response to urbanization

Urbanization can cause species to adjust their sexual displays, as the effectiveness of mating signals is impacted by environmental conditions. Despite many examples showing that mating signals in urban conditions differ from those in rural conditions, we do not know whether these differences provide a combined reproductive and survival benefit to the urban phenotype. Here we show that male túngara frogs have increased the conspicuousness of their calls, which is under strong sexual and natural selection by signal receivers, as an adaptive response to city life. The urban phenotype consequently attracts more females than the forest phenotype, while avoiding the costs imposed by eavesdropping bats and midges, which we show are rare in urban areas. Finally, we show in a translocation experiment that urban frogs can reduce risk of predation and parasitism when moved to the forest, but that forest frogs do not increase their sexual attractiveness when moved to the city. Our findings thus reveal that urbanization can rapidly drive adaptive signal change via changes in both natural and sexual selection pressures.

Data from: Phenotypic selection on floral traits in an urban landscape

Native species are increasingly living in urban landscapes associated with abiotic and biotic changes that may influence patterns of phenotypic selection. However, measures of selection in urban and non-urban environments, and exploration of the mechanisms associated with such changes, are uncommon. Plant-animal interactions have played a central role in the evolution of flowering plants and are sensitive to changes in the urban landscape, and thus provide opportunities to explore how urban environments modify selection. We evaluated patterns of phenotypic selection on floral and resistance traits of Gelsemium sempervirens in urban and non-urban sites. The urban landscape had increased florivory and decreased pollen receipt, but showed only modest differences in patterns of selection. Directional selection for one trait, larger floral display size, was stronger in urban compared to non-urban sites. Neither quadratic nor correlational selection significantly differed between urban and non-urban sites. Pollination was associated with selection for larger floral display size in urban compared to non-urban sites, due to differences in the translation of pollination into seeds rather than pollinator selectivity. Thus, our data suggest that urban landscapes may not result in sweeping differences in phenotypic selection but rather modest differences for some traits, potentially mediated by species interactions.

Data from: Nitrogen fertilization differentially enhances nodulation and host growth of two invasive legume species in an urban environment

Invasive plants negatively impact native communities by altering ecosystem processes and reducing species diversity. Plants in the legume family are overrepresented among invasive taxa and establish in disturbed environments common in urban ecosystems. Mutualisms with rhizobia and anthropogenic activities, such as nitrogen fertilization, may be key mechanisms driving legume invasions of urban habitats. Moreover, legume species and genetic lineages within species may vary in their responses to nitrogen fertilization, making some more likely to invade than others. Despite this threat, it remains unclear whether nitrogen fertilization impacts mutualism and plant growth traits of invasive legumes in urban environments, and whether these effects depend on the genetic origin of invaders. We conducted a common garden experiment using two widespread, invasive legume species, Medicago sativa and Trifolium pratense, to test the effects of species, genetic origin of lineages within species, and nitrogen fertilization on the mutualism. Soil nitrogen was manipulated and effects on traits associated with the mutualism (nodule traits) and plant growth were quantified. Nitrogen fertilization improved nodule traits and host growth for both species, but M. sativa and certain genetic lineages of this species benefited more from fertilization than any of the tested T. pratense lineages. This work reveals how anthropogenic activities alter mutualism traits and plant growth in urban environments, potentially facilitating invasions by leguminous taxa. Because species and lineages varied in the strength of their responses to fertilization, over time some invading legumes may outcompete other plant species or lineages, leading to differential impacts on native communities in urban environments.

opencc-zeroDec 2019View details →

Data from: A place-based participatory mapping approach for assessing cultural ecosystem services in urban green space

1. Cultural Ecosystem Services (CES) encompass a range of social, cultural and health benefits to local communities, for example recreation, spirituality, a sense of place and local identity. However, these complex and place-specific CES are often overlooked in rapid land management decisions and assessed using broad, top–down approaches. 2. We use the Toolkit for Ecosystem Service Site-based Assessment (TESSA) to examine a novel approach to rapid assessment of local CES provision using inductive, participatory methods. We combined free-listing and participatory geographic information systems (GIS) techniques to quantify and map perceptions of current CES provision of an urban green space. The results were then statistically compared with those of a proposed alternative scenario with the aim to inform future decision-making. 3. By identifying changes in the spatial hotspots of CES in our study area, we revealed a spatially-specific shift toward positive sentiment regarding several CES under the alternative state with variance across demographic and stakeholder groups. Response aggregations in areas of proposed development reveal previously unknown stakeholder preferences to local decision-makers and highlight potential trade-offs for conservation management. Free-listed responses revealed deeper insight into personal opinion and context. 4. This work serves as a useful case study on how the perceptions and opinions of local people regarding local CES could be accounted for in the future planning of an urban greenspace and how thorough analysis of CES provision is important to fully-inform local-scale conservation and planning for the mutual benefit of local communities and nature.

Data from: From forest to city: Urbanization modulates relative abundance of anti-predator coloration

Increased urbanization has resulted in community changes including alteration of predator communities. Little is known, however, about how such changes affect morphological anti-predator traits. Given the importance of coloration in predator avoidance, this trait in particular is expected to be susceptible to novel selective environments in urban areas. Here we investigate the coloration pattern of a Neotropical anuran species, the túngara frog (Engystomops pustulosus), along an urbanization gradient. Túngara frogs have two distinct color patterns (unstriped and striped) which we found to occur at different frequencies along an urbanization gradient. Striped individuals increased in frequency with urbanization. To assess the strength of selection imposed by predators on the two color morphs, we deployed clay models of túngara frogs in forest and semi-urban populations. In addition, we examined microhabitat selection by individuals of the different morphs. We found higher predation rates associated with urbanization than forested areas. In particular, frogs from forested habitats had lower number of attacks by avian predators. Contrary to our predictions, however, predation rates were similar for both color morphs independent of urbanization. Also, coloration of the frogs did not affect their microhabitat preference. Overall, túngara frogs are more likely to have a striped coloration pattern in semi-urban areas where predation by birds is higher than in the forest. Our findings suggest that factors other than predation pressure shape the coloration pattern of urban frogs and emphasize the complex nature of effects that anthropogenic changes in habitat and predator communities may have on prey morphology.

Data from: Current and historical land use influence soil-based ecosystem services in an urban landscape

Urban landscapes are increasingly recognized as providing important ecosystem services (ES) to their occupants. Yet, urban ES assessments often ignore the complex spatial heterogeneity and land-use history of cities. Soil-based services may be particularly susceptible to land-use legacy effects. We studied indicators of three soil-based ES – carbon storage, water quality regulation, and runoff regulation – in a historically agricultural urban landscape and asked: (1) How do ES indicators vary with contemporary land cover and time since development? (2) Do ES indicators vary primarily among land-cover classes, within land-cover classes, or within sites? (3) What is the relative contribution of urban land-cover classes to potential citywide ES provision? We measured biophysical indicators (soil carbon (C), available phosphorus (P), and saturated hydraulic conductivity (Ks)) in 100 sites across 5 land-cover classes, spanning an ~125 year gradient of time since development within each land-cover class. Potential for ES provision was substantial in urban green spaces, including developed land. Runoff regulation services (high Ks) were highest in forests; water quality regulation (low P) was highest in open spaces and grasslands; and open spaces and developed land (e.g., residential yards) had the highest C storage. In developed land covers, both C and P increased with time since development, indicating effects of historical land-use on contemporary ES and tradeoffs between two important ES. Among-site differences accounted for a high proportion of variance in soil properties in forests, grasslands, and open space, while residential areas had high within-site variability – underscoring the leverage city residents have to improve urban ES provision. Developed land covers contributed most ES supply at the citywide scale, even after accounting for potential impacts of impervious surfaces. Considering the full mosaic of urban green space and its history is needed to estimate the kinds and magnitude of ES provided in cities, and to augment regional ES assessments that often ignore or underestimate urban ES supply.

opencc-zeroDec 2016View details →

Data from: Divergent habitat use of two urban lizard species

Faunal responses to anthropogenic habitat modification represent an important aspect of global change. In Puerto Rico, two species of arboreal lizard, Anolis cristatellus and A. stratulus, are commonly encountered in urban areas, yet seem to use the urban habitat in different ways. In this study, we quantified differences in habitat use between these two species in an urban setting. For each species, we measured habitat use and preference, and the niche space of each taxon, with respect to manmade features of the urban environment. To measure niche space of these species in an urban environment, we collected data from a total of six urban sites across four different municipalities on the island of Puerto Rico. We quantified relative abundance of both species, their habitat use, and the available habitat in the environment to measure both microhabitat preference in an urban setting, as well as niche partitioning between the two different lizards. Overall, we found that the two species utilize different portions of the urban habitat. Anolis stratulus tends to use more "natural" portions of the urban environment (i.e., trees and other cultivated vegetation), whereas A. cristatellus more frequently uses anthropogenic structures. We also found that aspects of habitat discrimination in urban areas mirror a pattern measured in prior studies for forested sites in which A. stratulus was found to perch higher than A. cristatellus and preferred lower temperatures and greater canopy cover. In our study, we found that the multivariate niche space occupied by A. stratulus did not differ from the available niche space in natural portions of the urban environment and in turn represented a subset of the niche space occupied by A. cristatellus. The unique niche space occupied by A. cristatellus corresponds to manmade aspects of the urban environment generally not utilized by A. stratulus. Our results demonstrate that some species are merely tolerant of urbanization while others utilize urban habitats in novel ways. This finding has implications for long-term persistence in urban habitats and suggests that loss of natural habitat elements may lead to nonrandom species extirpations as urbanization intensifies.

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.

Data from: Temperature accounts for the biodiversity of a hyperdiverse group of insects in urban Los Angeles

The urban heat island effect is a worldwide phenomenon that has been linked to species' distributions and abundances in cities. However, effects of urban heat on biotic communities are nearly impossible to disentangle from effects of land cover in most cases because hotter urban sites also have less vegetation and more impervious surfaces than cooler sites within cities. We sampled phorid flies, one of the largest, most biologically diverse families of true flies (Insecta: Diptera: Phoridae), at 30 sites distributed within the central Los Angeles Basin, where we found that temperature and the density of urban land cover are decoupled. Abundance, richness, and community composition of phorids inside urban Los Angeles were most parsimoniously accounted for by mean air temperature in the week preceding sampling. Sites with intermediate mean temperatures had more phorid fly individuals and higher richness. Communities were more even at urban sites with lower minimum temperatures and sites located further away from natural areas, suggesting that communities separated from natural source populations may be more homogenized. Species composition was best explained by minimum temperature. Inasmuch as warmer areas within cities can predict future effects of climate change, phorid fly communities are likely to shift non-linearly under future climates in more natural areas. Exhaustive surveys of biotic communities within cities, such as the one we describe here, can provide baselines for determining the effects of urban and global climate warming as they intensify.

Data from: Are signals of aggressive intent less honest in urban habitats?

How anthropogenic change affects animal social behavior, including communication is an important question. Urban noise often drives shifts in acoustic properties of signals but the consequences of noise for the honesty of signals – i.e. how well they predict signaler behavior – is unclear. Here we examine whether honesty of aggressive signaling is compromised in male urban song sparrows (Melospiza melodia). Song sparrows have two honest close-range signals: the low amplitude soft songs (an acoustic signal) and wing waves (a visual signal) but whether the honesty of these signals is affected by urbanization has not been examined. If soft songs are less effective in urban noise, we predict that they should predict attacks less reliably in urban habitats compared to rural habitats. We confirmed earlier findings that urban birds were more aggressive than rural birds and found that acoustic noise was higher in urban habitats. Urban birds still sang more soft songs than rural birds. High rates of soft songs and low rates of loud songs predicted attacks in both habitats. Thus, while urbanization has a significant effect on aggressive behaviors, it might have a limited effect on the overall honesty of aggressive signals in song sparrows. We also found evidence for a multimodal shift: urban birds tended to give proportionally more wing waves than soft songs than rural birds, although whether that shift is due to noise-dependent plasticity is unclear. These findings encourage further experimental study of the specific variables that are responsible for behavioral change due to urbanization.

Data from: Carbon dioxide and methane fluxes from different surface types in a created urban wetland

Many wetlands have been drained due to urbanization, agriculture, forestry or other purposes, which has resulted in losing their ecosystem services. To protect receiving waters and to achieve services such as flood control and stormwater quality mitigation, new wetlands are created in urbanized areas. However, our knowledge of greenhouse gas exchange in newly created wetlands in urban areas is currently limited. In this paper we present measurements carried out at a created urban wetland in boreal climate. We conducted measurements of ecosystem CO2 flux (NEE) and CH4 flux (FCH4) at the constructed stormwater wetland Gateway in Nummela, Vihti, Southern Finland using eddy covariance (EC) technique. The measurements were commenced the fourth year after construction and lasted for one full year and two subsequent growing seasons. Besides ecosystem scale fluxes measured by EC tower, the diffusive CO2 and CH4 fluxes from the open-water area (Fw_CO2 and Fw_CH4, respectively) were modelled based on measurements of CO2 and CH4 concentration in the water. Fluxes from vegetated area were estimated by applying a simple mixing model using above-mentioned fluxes and footprint-weighted fractional area. The half-hourly footprint-weighted contribution of diffusive fluxes from open water ranged from 0 to 25.5 % in year 2013. The annual NEE of the studied wetland was 8.0 g C-CO2 m-2 yr-1 with the 95 % confidence interval between -18.9 and 34.9 g C-CO2 m-2 yr-1 and FCH4 was 3.9 g C-CH4 m-2 yr-1 with the 95 % confidence interval between 3.75 and 4.07 g C-CH4 m-2 yr-1. The ecosystem sequestered CO2 during summer months (June-August), while the rest of the year it was a CO2 source. CH4 displayed strong seasonal dynamics, higher in summer and lower in winter, with a sporadic emission episode in the end of May 2013. Both CH4 and CO2 fluxes, especially those obtained from vegetated area, exhibited strong diurnal cycle during summer with synchronized peaks around noon. The annual Fw_CO2 was 297.5 g C-CO2 m-2 yr-1 and Fw_CH4 was 1.73 g C-CH4 m-2 yr-1. The peak diffusive CH4 flux was 137.6 nmol C-CH4 m-2 s-1, which was synchronized with the FCH4. Overall, during the monitored time period, the established stormwater wetland had a climate warming effect with 0.263 kg CO2-eq m-2 yr-1 of which 89 % was contributed by CH4. The radiative forcing of the open-water exceeded the vegetation area (1.194 kg CO2-eq m-2 yr-1 and 0.111 kg CO2-eq m-2 yr-1, respectively), which implies that, when considering solely the climate impact of a created wetland over a 100-year horizon, it would be more beneficial to design and establish wetlands with large patches of emergent vegetation, and to limit the areas of open-water to the minimum necessitated by other desired ecosystem services.