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opencc-zeroAug 2019View details →

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: Barriers to access improved water and sanitation in poor peri-urban settlements of Abidjan, Côte d'Ivoire

Achieving access to safe water and sanitation still pose major challenges in urban areas of sub-Saharan Africa countries, despite all the progress achieved in the last decade. This study assessed the ability of populations living in poor peri-urban settlements to access improved water and sanitation and identified factors influencing this access, in order to guide sustainable mitigating solutions to address associated health and environmental risks. We conducted a cross-sectional study in six poor peri-urban settlements of Yopougon, the largest municipality of Abidjan. A total of 556 randomly selected households were included. The factors associated with access to improved water and sanitation were identified through explanatory models using multivariate logistic regression. A proportion of 25% of all households assessed did not have access to clean water and 57% lacked improved sanitation. Socioeconomic status and settlement characteristics appear as the main indicators of poor access to reliable water and sanitation in peri-urban settlements. The presence of the household head's wife at home was associated with greater access to clean water (OR = 3.57; 95% CI: 1.74, 7.31), thus highlighting the important role of women in ensuring access to clean water in these specific environments. Household size, education and religion were not significantly associated with the two considered outcomes. Women therefore should be involved at all levels of programming in water promotion in these settlements to improve the population's well-being. While religion does not appear to play an important role in access to water and sanitation, successful interventions should involve religious communities because of their large representation.

Data from: Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum)

Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multi-scale analysis to determine how landscape composition, configuration, and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side-by-side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analyzed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavorable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results, and shows how multi-scale analyses provide insight to scale-dependent processes.

opencc-zeroNov 2019View details →

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: Experimental small-scale flower patches increase species density but not abundance of small urban bees

1. Large flower plantings are often used to combat negative effects of habitat loss on pollinators, but whether these floral additions are effective at smaller scales remains unclear, particularly in urban settings. 2. To test the effectiveness of small-scale floral additions on enhancing urban bee populations, as well as their impact from one year to the next, different quantities of potted sweet alyssum (Lobularia maritima) flowers were placed across sites in Ann Arbor, Michigan for two consecutive years and the resulting Halictid bee visitors were monitored. 3. Overall we found the number of flowers added at the local level was significantly and positively correlated with small Halictid bee abundance and species density in an urban landscape. At smaller flower quantities dynamics were clearly linear, where incremental increases in number of flowers showed significant increases in bee abundance and species density. At larger quantities of floral additions, however, dynamics were nonlinear in that incremental increases in flower quantity had no effect on bee abundance and highly variable effects on bee species density. 4. When comparing the change in small Halictid bee abundance and species density from one year to the next, we found a significant increase in bee species density in the second year of small-scale floral additions, but no significant difference in bee abundance. 5. Synthesis and applications. Our results show that small flower plantings can have positive effects on small bee communities in urban systems even over a short period of time, and therefore confirm that encouraging citizens to plant flowers can be an effective conservation strategy for certain urban pollinator populations. In addition, our finding that smaller flower plantings may have higher impacts on small pollinators than larger plantings suggests resource managers interested in pollinator conservation should consider spreading multiple, smaller floral plantings across the urban landscape, rather than pooling all resources into one large flower patch.29-Nov-2017

opencc-zeroDec 2018View details →

Data from: Urbanization alters predator avoidance behaviors

1. Urbanization is considered the fastest growing form of global land use change and can dramatically modify habitat structure and ecosystem function. While ecological processes continue to operate within cities, urban ecosystems are profoundly different from their more natural counterparts. Thus, ecological predictions derived from more natural ecosystems are rarely generalizable to urban environments. 2. In this study we used data from a large-scale and long-term camera trapping project in Chicago IL, USA to determine whether urbanization alters predator avoidance behavior of urban prey species. 3. We studied three behavioral mechanisms often induced by the fear of predation (spatial distribution, daily activity patterns, and vigilance) of white-tailed deer (Odocoileus virginianus) and eastern cottontail (Sylvilagus floridanus) when coyote (Canis latrans) – an urban apex predator – was present in the same habitat patch. 4. We found no evidence of spatial segregation between coyote and either prey species. Furthermore, neither white-tailed deer nor eastern cottontail changed their daily activity or increased vigilance in urban areas when coyotes were present. Eastern cottontail, however, had their uppermost level of vigilance in highly urban sites when coyotes were absent. 5. Our study demonstrates that predator-prey dynamics might be modified in urban ecosystems – moving from what is traditionally thought of as a two-player system (predator and prey) to a three-player system (predator, prey, and people).

Data from: Water availability drives urban tree growth responses to herbivory and warming

1. Urban forests provide important ecosystem services to city residents, including pollution removal and carbon storage. Climate change and urbanization pose multiple threats to these services. However, how these threats combine to affect urban trees, and thus how to mitigate their effects, remains largely untested because multi-factorial experiments on mature trees are impractical. 2. We used a unique urban warming experiment paired with a laboratory chamber experiment to determine how three of the most potentially damaging factors associated with global change for urban and rural trees—warming, drought, and insect herbivory—affect growth of Quercus phellos (willow oak), the most commonly-planted large shade tree in the southeastern US, which is known for its resilience to these potential stressors. 3. In a previous study, we found that the urban heat island effect was associated with reduced growth of Q. phellos and higher abundance of Parthenolecanium scale insects, key pests of oaks in cities. Here, we tested the hypothesis that tree water stress is the mechanism for these effects of warming. We found evidence that water stress is a major, interactive factor reducing urban tree growth, but found no evidence that water stress is associated with Parthenolecanium survival or abundance. Warming and Parthenolecanium only reduced growth in Q. phellos saplings that were simultaneously water stressed. 4. Synthesis and applications. Across many temperate cities worldwide, urban trees grow less than rural trees. Our results point to water stress as the most likely driver for this pattern. Importantly, we found that water stress both reduces tree growth on its own and exacerbates effects of warming and insect pests on tree growth. Therefore, management strategies targeted at increasing tree hydration in cities may reduce effects of these three key stressors that are expected to intensify with further urbanization and climate change.

opencc-zeroDec 2015View details →

Data from: Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to man, and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180 km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city. We sampled M. natalensis across 10 localities, and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the Isolation-with-Migration model implemented in IMa2 we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban-source to rural-sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2NeM = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.

opencc-zeroJun 2019View details →

Data from: Leaf-litter decomposition and macroinvertebrate assemblages along an urban stream gradient in Puerto Rico

Urbanization is a major land use form that has large impacts on ecosystems. Urban development in the watershed impacts stream ecosystems by increasing nutrient and organic matter loads, altering hydrology, and reducing biodiversity. Puerto Rico is an ideal location to assess and monitor the effects of urbanization on streams, because it is increasingly urbanized and streams do not receive inputs of untreated sewage, characteristic of many other tropical urban areas. The objective of this study was to determine how leaf-litter decomposition and aquatic macroinvertebrate assemblages varied along a tropical urban gradient. We conducted the study in the Río Piedras watershed, San Juan Metropolitan Area, in six low order streams that formed an urban gradient ranging from 10 to 70% urban land cover. At each stream, we placed six 5g leaf bags of Ficus longifolia in three different pools and collected one bag on each sampling date. Decomposition rates were fast in forested streams (range 0.021 – 0.039 day-1) and decreased with increasing urbanization (range 0.007 – 0.008 day-1). Rates were strongly and negatively correlated with percent impervious surface cover (R= 0.81, p=0.01). Functional feeding group diversity was higher in forested streams, with the presence of shredders. Decomposition rates were significantly and positively correlated with functional feeding group diversity and abundance (R= 0.66, p= 0.04). Overall, our results show that urbanization affected the environment and macroinvertebrate diversity resulting in large negative effects on stream ecosystem function.

opencc-zeroAug 2019View details →

Data from: Human–Cougar interactions in the wildland–urban interface of Colorado's front range

As human populations continue to expand across the world, the need to understand and manage wildlife populations within the wildland–urban interface is becoming commonplace. This is especially true for large carnivores as these species are not always tolerated by the public and can pose a risk to human safety. Unfortunately, information on wildlife species within the wildland–urban interface is sparse, and knowledge from wildland ecosystems does not always translate well to human‐dominated systems. Across western North America, cougars (Puma concolor) are routinely utilizing wildland–urban habitats while human use of these areas for homes and recreation is increasing. From 2007 to 2015, we studied cougar resource selection, human–cougar interaction, and cougar conflict management within the wildland–urban landscape of the northern Front Range in Colorado, USA. Resource selection of cougars within this landscape was typical of cougars in more remote settings but cougar interactions with humans tended to occur in locations cougars typically selected against, especially those in proximity to human structures. Within higher housing density areas, 83% of cougar use occurred at night, suggesting cougars generally avoided human activity by partitioning time. Only 24% of monitored cougars were reported for some type of conflict behavior but 39% of cougars sampled during feeding site investigations of GPS collar data were found to consume domestic prey items. Aversive conditioning was difficult to implement and generally ineffective for altering cougar behaviors but was thought to potentially have long‐term benefits of reinforcing fear of humans in cougars within human‐dominated areas experiencing little cougar hunting pressure. Cougars are able to exploit wildland–urban landscapes effectively, and conflict is relatively uncommon compared with the proportion of cougar use. Individual characteristics and behaviors of cougars within these areas are highly varied; therefore, conflict management is unique to each situation and should target individual behaviors. The ability of individual cougars to learn to exploit these environments with minimal human–cougar interactions suggests that maintaining older age structures, especially females, and providing a matrix of habitats, including large connected open‐space areas, would be beneficial to cougars and effectively reduce the potential for conflict.

Data from: Local and landscape drivers of predation services in urban gardens

In agroecosystems, local and landscape features, as well as natural enemy abundance and richness are significant predictors of predation services that may result in biological control of pests. Despite the increasing importance of urban gardening for provisioning of food to urban populations, most urban gardeners suffer from high pest problems, and have little knowledge about how to manage their plots to increase biological control services. We examined the influence of local, garden scale (i.e. herbaceous and arboreal vegetation abundance and diversity, ground cover) and landscape (i.e. landscape diversity and surrounding land use types) characteristics on predation services provided by naturally occurring predators in 19 urban gardens in the California central coast. We introduced sentinel pests (moth eggs and larvae and pea aphids) onto greenhouse-raised plants taken to gardens and assigned to open or bagged (predator exclosure) treatments. We found high predation rates with between 40-90% of prey items removed in open treatments. Predation services varied with local and landscape factors, but significant predictors differed by prey species. Predation of eggs and aphids increased with vegetation complexity in gardens, but larvae predation declined with vegetation complexity. Smaller gardens experienced higher predation services, likely due to increases in predator abundance in smaller gardens. Several ground cover features influenced predation services. In contrast to patterns in rural agricultural landscapes, predation on aphids declined with increases in landscape diversity. In sum, we report the relationships between several local management factors, as well as landscape surroundings, and implications for garden management.

opencc-zeroDec 2015View details →

Data from: Effect of acute stressor on reproductive behavior differs between urban and rural birds

The life-history trade-off between self-maintenance and reproduction posits that investment in one function decreases investment in the other. Manipulating the costs and benefits of functions involved in a trade-off may alter this interaction. Here we ask whether investment in self-maintenance during a stress response alters territorial behavior in wild Dark-eyed Juncos and whether rural and urban birds, which are known to differ in the magnitude of the stress response (greater in rural), also differ in the degree to which stress reduces territorial behavior. In rural and urban habitats, we measured territorial behavior using song playback, followed by either an acute stressor (capture and collection of a blood sample) or a nonstressful control situation. The following day, we again measured territorial behavior, predicting greater reduction in territorial behavior in individuals exposed to the stressor but a lesser reduction in territorial behavior in the urban as compared to the rural environment. We further assessed individual and population differences in response to stressors by measuring flight initiation distance, breath rate, and corticosterone levels in the blood. The rural population had a higher physiological and behavioral stress response than the urban population, and acute capture stress had a lasting (24 h) negative effect on territorial behavior, but only in the rural habitat. However, individual-level differences in measures of the stress response did not explain variation in the impact of stress on territorial behavior. Our findings show that stressors can have a negative effect on territorial behavior, but that this effect may differ between populations that vary in their stress ecology.

Data from: Consumer-resource interactions along urbanization gradients drive natural selection

<p>Urbanization is an important component of global change. Urbanization affects species interactions, but the evolutionary implications are rarely studied. We investigate the evolutionary consequences of a common pattern: the loss of high trophic-level species in urban areas. Using a gall-forming fly, Eurosta solidaginis, and its natural enemies that select for opposite gall sizes, we test for patterns of enemy loss, selection, and local adaptation along five urbanization gradients. Eurosta declined in urban areas, as did predation by birds, which preferentially consume gallmakers that induce large galls. These declines were linked to changes in habitat availability, namely reduced forest cover in urban areas. Conversely, a parasitoid which attacks gallmakers that induce small galls was unaffected by urbanization. Changes in patterns of attack by birds and parasitoids resulted in stronger directional selection, but loss of stabilizing selection in urban areas, a pattern which we suggest may be general. Despite divergent selective regimes, gall size did not very systematically with urbanization, suggesting but not conclusively demonstrating that environmental differences, gene flow, or drift, may have prevented the adaptive divergence of phenotypes. We argue that the evolutionary effects of urbanization will have predictable consequences for patterns of species interactions and natural selection.</p>

opencc-zeroDec 2010View details →

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.

opencc-zeroDec 2015View details →

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

Data from: Urban versus forest ecotypes are not explained by divergent reproductive selection

Increasing urbanisation offers a unique opportunity to study adaptive responses to rapid environmental change. Numerous studies have demonstrated phenotypic divergence between urban and rural organisms. However, comparing the direction and magnitude of natural selection between these environments has rarely been attempted. Using seven years of nest-box breeding monitoring of great tits (Parus major) in the city of Montpellier and in a nearby oak forest, we find phenotypic divergence in four morphological and two life-history traits between urban and forest birds. We then measure reproductive selection on these traits, and compare selection between the habitats. Urban birds had significantly smaller morphological features than their rural counterparts, with shorter tarsus, lower body mass and smaller wing and tail lengths relative to their overall body size. While urban female tarsus length was under stabilising selection, and forest males show positive selection for tarsus length and negative selection for body mass, selection gradients were significantly divergent between habitats only for body mass. Urban great tits also had earlier laying dates and smaller clutches. Surprisingly, we found selection for earlier laying date in the forest but not in the city. Conversely, we detected no linear selection on clutch size in the forest, but positive selection on clutch size in the urban habitat. Overall, these results do not support the hypothesis that contemporary reproductive selection explains differences in morphology and life history between urban and forest breeding great tits. We discuss how further experimental approaches will help confirm whether the observed divergence is maladaptive while identifying the environmental drivers behind it.

opencc-zeroDec 2014View details →

Data from: Seasonally varying contributions to urban CO2 in the Chicago, IL, USA region: insights from a high-resolution CO2 concentration and δ13C record

Understanding urban carbon cycling is essential given that cities sustain 54% of the global population and contribute 70% of anthropogenic CO2 emissions. When combined with CO2 concentration measurements ([CO2]), stable carbon isotope analyses (δ13C) can differentiate sources of CO2, including ecosystem respiration and combustion of fossil fuels, such as petroleum and natural gas. In this study, we used a wavelength scanned-cavity ringdown spectrometer to collect ~2x106 paired measurements for [CO2] and δ13C values in Evanston, IL for August 2011 through February 2012. Evanston is located immediately north of Chicago, IL, the third largest city in the United States. The measurements represent one of the longest records of urban [CO2] and δ13C values thus far reported. We also compiled local meteorological information, as well as complementary [CO2] and δ13C data for background sites in Park Falls, WI and Mauna Loa, HI. We use the dataset to examine how ecosystem processes, fossil fuel usage, wind speed, and wind direction control local atmospheric [CO2] and δ13C in a midcontinent urban setting on a seasonal to daily basis. On average, [CO2] and δ13C values in Evanston were 16–23 ppm higher and 0.97–1.13‰ lower than the background sites. While seasonal [CO2] and δ13C values generally followed broader northern hemisphere trends, the difference between Evanston and the background sites was larger in winter versus summer. Mixing calculations suggest that ecosystem respiration and petroleum combustion equally contributed CO2 in excess of background during the summer and that natural gas combustion contributed 80%–94% of the excess CO2 in winter. Wind speed and direction strongly influenced [CO2] and δ13C values on an hourly time scale. The highest [CO2] and lowest δ13C values occurred at wind speeds <3 m s−1 and when winds blew from the northwest, west, and south over densely populated neighborhoods.

Data from: Fat and happy in the city: eastern chipmunks in urban environments

Cities are rapidly expanding, and wildlife may experience different selection pressures in urban environments when compared to natural habitats. Phenotypic differences between urban and natural populations may occur because of the altered urban environment. Behavior, the activity of the hypothalamic-pituitary-adrenal (HPA) axis and body condition can be expected to differ between urban and natural habitats. We used the eastern chipmunk (Tamias striatus) to test for differences in behavior assayed from an open field test, hair and fecal cortisol concentrations, and body condition (size-corrected body mass), predicting that urban chipmunks would exhibit more exploratory behavior, higher cortisol concentrations, and higher body condition, than their counterparts from natural habitats. We sampled eastern chipmunks in 2 urban areas paired with natural habitats and subjected adult chipmunks to an open field test, collected hair and fecal samples for the determination of cortisol concentrations, and measured body size and body mass to estimate body condition. Eastern chipmunks in urban habitats had significantly different behavior, tending toward reduced locomotion and grooming, and greater latency, than their counterparts from natural habitats. Urban chipmunks also had lower fecal cortisol concentrations than those from natural habitats, and female chipmunks were in better body condition when captured in urban habitats. These results suggest that urban habitats may be relatively benign for urban chipmunks, perhaps because of reduced need for exploration and the availability of anthropogenic food subsidies associated with urban environments.

Data from: Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages

Annelids (Lumbricidae and Enchytraeidae) and nematodes are common soil organisms and play important roles in organic matter decomposition, nutrient cycling and creation of soil structure and porosity. However, these three groups have rarely been studied together and only few studies exist for urban soils. We studied the diversity and community composition of annelids and nematodes in soils spanning more than two centuries of urban soil development in Neuchâtel (Switzerland) and assessed the relationships 1) among these three groups and 2) between each group and environmental (physical, chemical and functional) characteristics of soils and soil age. While the groups of environmental variables were correlated (Mantel tests) no correlation was found between pairs of soil fauna groups and between each soil fauna group and environmental variables. More specifically, redundancy analyses showed that earthworm assemblages were best correlated with soil bulk density and with soil depth, the latter being positively correlated with soil age. Enchytraeid assemblages and the proportion of enchytraeid r-strategists were respectively best correlated with soil carbonate content and negatively correlated with soil age. Nematodes assemblages were best correlated with soil water content. Moreover, relationships between pairs of soil biota groups, and between each group and environmental (physical, chemical and functional) variables, varied along the soil age gradient (moving window analysis). This study provides new knowledge on urban soil biodiversity and how environmental conditions can influence soil diversity and community patterns in the urban context. The contrasted community patterns of earthworms, enchytraeids and nematodes in urban soils of different ages and their different ecological roles suggest that they represent potential complementary indicators of soil quality and functioning such as soil formation and organic matter dynamics.

Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient

Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city (Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site-level but not at the nest-level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.