Fine Geographic Scale Research Articles

Internal and contextual drivers of dairy restructuring: evidence from French mountainous areas and post‐quota prospects

AbstractThe end of the milk quota system in Europe has resulted in substantial structural changes to the dairy industry, calling its future into question, especially in mountainous areas. This study analyzes the internal and contextual factors that influence dairy restructuring in French mountainous areas. Three complementary logit models are used to specify farmer decisions (e.g., dairy production exit, stability, and growth). Original and exhaustive geo‐located administrative datasets are combined to create a farm longitudinal dataset and characterize farm‐restructuring patterns on a fine geographical scale. Farm size, corporate legal status, and specialization are positively associated with farm growth. Viable diversification strategies through either farm processing or agro‐environmental scheme contracting are also highlighted. Farm sustainability is supported by the economic success of the local industry and the propensity to adopt extensive practices. With respect to public policy, dairy policy appears to have the strongest impact. Thus, the liberalization of dairy policy threatens the future of dairy farming, particularly in areas with low milk density and no production under labels. This work calls for a policy that promotes the collective dimension of dairy farm performance. The current rural development policy alone may be insufficient to support farms’ long‐term sustainability.

Spatial variation in climate mediates gene flow across an island archipelago.

High levels of gene flow among partially isolated populations can overwhelm selection and limit local adaptation. This process, known as "gene swamping," can homogenize genetic diversity among populations and reduce the capacity of a species to withstand rapid environmental change. We studied brown anole lizards (Anolis sagrei) distributed across seven islands in The Bahamas. We used microsatellite markers to estimate gene flow among islands and then examined the correlation between thermal performance and island temperature. The thermal optimum for sprint performance was correlated with both mean and maximum island temperature, whereas performance breadth was not correlated with any measure of temperature variation. Gene flow between islands decreased as the difference between mean island temperatures increased, even when those islands were adjacent to one another. These data suggest that phenotypic variation is the result of either (1) local genetic adaptation with selection against immigrants maintaining variation in the thermal optimum, (2) irreversible forms of adaptive plasticity such that immigrants have reduced fitness, or (3) an interaction between fixed genetic differences and plasticity. In general, the patterns of gene flow we observed suggest that local thermal environments represent important ecological filters that can mediate gene flow on relatively fine geographic scales.

Genetic diversity and population structure of the Asian green mussel Perna viridis in South China Sea based on microsatellite markers

The green mussel, Perna viridis is ecologically and economically important in the coastal region of the South China Sea. Determining its population genetic structure at this fine geographic scale will help sustainable management of natural stocks. In this study, we examined the genetic diversity and population genetic structure of P. viridis from four locations in the South China Sea (n = 45–48) using nine microsatellite loci. The results showed moderate levels of genetic diversity in all four samples (mean A = 13.222–14.000, mean Ae = 7.092–7.571, mean Ar = 12.894–13.746, mean Ho = 0.596–0.656, mean He = 0.690–0.733) and a large effective population size estimate for the pooled sample (total Ne estimates = infinity, 95% CI = 1869.0-infinity). We did not detect any sign of recent bottleneck events in P. viridis populations in the South China Sea. The conventional and a model-based analysis reveal low, non-significant genetic divergence among the four samples (FST = − 0.001–0.005, P > 0.05/6). The results obtained from this study can provide valuable genetic information for the conservation and fishery management of P. viridis by retaining the high Ne estimates.

Fine-scale genetic structure among greater sage-grouse leks in central Nevada.

BackgroundMating systems that reduce dispersal and lead to non-random mating might increase the potential for genetic structure to arise at fine geographic scales. Greater sage-grouse (Centrocercus urophasianus) have a lek-based mating system and exhibit high site fidelity and skewed mating ratios. We quantified population structure by analyzing variation at 27,866 single-nucleotide polymorphisms in 140 males from ten leks (within five lek complexes) occurring in a small geographic region in central Nevada.ResultsLek complexes, and to a lesser extent individual leks, formed statistically identifiable clusters in ordination analyses, providing evidence for fine-scale geographic genetic differentiation. Lek geography predicted genetic differentiation even at a small geographic scale, which could be sharpened by strong site fidelity. Relatedness was also higher among individuals within lek complexes (and leks), suggesting that reproductive skew, where few males participate in most of the successful matings, could also potentially contribute to genetic differentiation. Models incorporating a habitat resistance surface as a proxy for potentially reduced movement due to landscape features indicated that both geographic distance and habitat suitability (i.e. preferred habitat) predicted genetic structure, with no significant effect of man-made barriers to movement (i.e. power lines and roads). Finally, we illustrate how data sets containing fewer loci (<4000) had less statistical precision and failed to detect the full degree of genetic structure.ConclusionOur results suggest that habitat features and lek site geography of sage-grouse shape fine scale genetic structure, and highlight how larger data sets can have increased precision and accuracy for quantifying ecologically relevant genetic structure over small geographic scales.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0702-4) contains supplementary material, which is available to authorized users.

Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan.

As a result of the combination of great linguistic and cultural diversity, the highland populations of Daghestan present an excellent opportunity to test the hypothesis of language-gene coevolution at a fine geographic scale. However, previous genetic studies generally have been restricted to uniparental markers and have not included many of the key populations of the region. To improve our understanding of the genetic structure of Daghestani populations and to investigate possible correlations between genetic and linguistic variation, we analyzed ~550,000 autosomal single nucleotide polymorphisms, phylogenetically informative Y chromosome markers and mtDNA haplotypes in 21 ethnic Daghestani groups. We found high levels of population structure in Daghestan consistent with the hypothesis of long-term isolation among populations of the highland Caucasus. Highland Daghestani populations exhibit extremely high levels of between-population diversity for all genetic systems tested, leading to some of the highest FST values observed for any region of the world. In addition, we find a significant positive correlation between gene and language diversity, suggesting that these two aspects of human diversity have coevolved as a result of historical patterns of social interaction among highland farmers at the community level. Finally, our data are consistent with the hypothesis that most Daghestanian-speaking groups descend from a common ancestral population (~6000-6500 years ago) that spread to the Caucasus by demic diffusion followed by population fragmentation and low levels of gene flow.

Big Data and Big Cities: The Promises and Limitations of Improved Measures of Urban Life

New, “big” data sources allow measurement of city characteristics and outcome variables higher frequencies and finer geographic scales than ever before. However, big data will not solve large urban social science questions on its own. Big data has the most value for the study of cities when it allows measurement of the previously opaque, or when it can be coupled with exogenous shocks to people or place. We describe a number of new urban data sources and illustrate how they can be used to improve the study and function of cities. We first show how Google Street View images can be used to predict income in New York City, suggesting that similar image data can be used to map wealth and poverty in previously unmeasured areas of the developing world. We then discuss how survey techniques can be improved to better measure willingness to pay for urban amenities. Finally, we explain how Internet data is being used to improve the quality of city services.

Estimation of property loss and business interruption loss caused by storm surge inundation due to climate change: a case of Typhoon Vera revisit

This paper estimates property loss and business interruption loss under scenarios of storm surge inundation to explore the economic impact of climate change on Ise Bay, Japan. Scenarios-based analyses are conducted with respect to Typhoon Vera, which caused the most severe storm surge in the recorded history of Japan in 1959. Four different hazard scenarios are chosen from a series of typhoon storm surge inundation simulations: Typhoon Vera’s landfall with respect to the condition of the past seawall; Typhoon Vera’s landfall with respect to the condition of the current seawall; intensifying Typhoon Vera, but retaining its original tracks; and intensifying Typhoon Vera, but choosing the worst tracks from various possible typhoon tracks. Our economic loss estimation takes advantage of fine geographical scale census and economic census data that enable us to understand the spatial distribution of property loss and business interruption loss as well as identify the most potentially affected areas and business sectors on a sub-city scale. By comparing the property loss and business interruption loss caused by different hazard scenarios, the effect of different seawalls is evaluated and the economic impact of future climate change is estimated. The results indicate that although the current seawall can considerably reduce the scale of losses, climate change can cause Ise Bay to experience more serious storm surge inundation. Moreover, the resulting economic losses would increase significantly owing to a combination of climate change and the worst track scenario. It is, therefore, necessary to consider more countermeasures to adapt to climate change in this area.

Host behaviour drives parasite genetics at multiple geographic scales: population genetics of the chewing louse, Thomomydoecus minor.

Pocket gophers and their symbiotic chewing lice form a host-parasite assemblage known for a high degree of cophylogeny, thought to be driven by life history parameters of both host and parasite that make host switching difficult. However, little work to date has focused on determining whether these life histories actually impact louse populations at the very fine scale of louse infrapopulations (individuals on a single host) at the same or at nearby host localities. We used microsatellite and mtDNA sequence data to make comparisons of chewing-louse (Thomomydoecus minor) population subdivision over time and over geographic space where there are different potential amounts of host interaction surrounding a zone of contact between two hybridizing pocket-gopher subspecies. We found that chewing lice had high levels of population isolation consistent with a paucity of horizontal transmission even at the very fine geographic scale of a single alfalfa field. We also found marked genetic discontinuity in louse populations corresponding with host subspecies and little, if any, admixture in the louse genetic groups even though the lice are closely related. The correlation of louse infrapopulation differentiation with host interaction at multiple scales, including across a discontinuity in pocket-gopher habitat, suggests that host behaviour is the primary driver of parasite genetics. This observation makes sense in light of the life histories of both chewing lice and pocket gophers and provides a powerful explanation for the well-documented pattern of parallel cladogenesis in pocket gophers and chewing lice.

Empirical distributions of vehicle use and fuel efficiency across space: Implications of asymmetry for measuring policy incidence

Concerns about local air pollution and climate change have prompted all levels of government to consider a variety of policies to reduce vehicle dependence and fuel consumption, as the transportation sector is one of the largest sources of local and global emissions. Because many of the policy options under consideration are market-based (e.g., gasoline tax, carbon tax), it is important to consider how the impacts would vary across space and affect different subpopulations. Evaluating incidence is relevant for both the expected costs and benefits of a particular policy, however detailed data on vehicle-miles traveled (VMT) and fuel consumption allowing for the distributions of these variables to be estimated at a fine geographic scale is rarely available. This paper uses a unique dataset with more than 20million vehicles in California to derive estimates of VMT and fuel consumption in order to examine the spatial distribution of impacts for an increase in the price of gasoline as well as the consequences of using different statistics for policy evaluation. Results show that VMT and fuel consumption distributions are not symmetrically distributed and vary significantly within transportation planning regions. To understand the potential implications of this asymmetry, we do a back of the envelope comparison using the mean and mode of the VMT or fuel consumption distribution for policy analysis. We find that assuming a symmetric distribution can lead to a divergence of 20–40% from the estimates based on the empirical distribution. Our results, therefore, introduce caution in interpreting the incidence of policies targeting the transportation sector based on averages.

Fine-scale genetic structure of Triatoma infestans in the Argentine Chaco

The patterns of genetic structure in natural populations provide essential information for the improvement of pest management strategies including those targeting arthropod vectors of human diseases. We analyzed the patterns of fine-scale genetic structure in Triatoma infestans in a well-defined rural area close to Pampa del Indio, in the Argentine Arid-Humid Chaco transition, where a longitudinal study on house infestation and wing geometric morphometry is being conducted since 2007. A total of 228 insects collected in 16 domestic and peridomestic sites from two rural communities was genotyped for 10 microsatellite loci and analyzed. We did not find departures from Hardy–Weinberg expectations in collection sites, with three exceptions probably due to null alleles and substructuring. Domestic sites were more variable than peridomestic sites suggesting the presence of older bug populations in domestic sites or higher effective population sizes. Significant genetic structure was detected using F-statistics, a discriminant analysis of principal components and Bayesian clustering algorithms in an area of only 6.32km2. Microsatellite markers detected population structuring at a finer geographic scale (180–6300m) than a previous study based on wing geometric morphometry (>4000m). The spatial distribution of genetic variability was more properly explained by a hierarchical island than by an isolation-by-distance model. This study illustrates that, despite more than a decade without vector control interventions enhancing differentiation, genetic structure can be detected in T. infestans populations, particularly applying spatial information. This supports the potential of genetic studies to provide key information for hypothesis testing of the origins of house reinfestation.

Environmental gap analysis to prioritize conservation efforts in eastern Africa.

Countries in eastern Africa have set aside significant proportions of their land for protection. But are these areas representative of the diverse range of species and habitats found in the region? And do conservation efforts include areas where the state of biodiversity is likely to deteriorate without further interventions? Various studies have addressed these questions at global and continental scales. However, meaningful conservation decisions are required at finer geographical scales. To operate more effectively at the national level, finer scale baseline data on species and on higher levels of biological organization such as the eco-regions are required, among other factors. Here we adopted a recently developed high-resolution potential natural vegetation (PNV) map for eastern Africa as a baseline to more effectively identify conservation priorities. We examined how well different potential natural vegetations (PNVs) are represented in the protected area (PA) network of eastern Africa and used a multivariate environmental similarity index to evaluate biases in PA versus PNV coverage. We additionally overlaid data of anthropogenic factors that potentially influence the natural vegetation to assess the level of threat to different PNVs. Our results indicate substantial differences in the conservation status of PNVs. In addition, particular PNVs in which biodiversity protection and ecological functions are at risk due to human influences are revealed. The data and approach presented here provide a step forward in developing more transparent and better informed translation from global priorities to regional or national implementation in eastern Africa, and are valid for other geographic regions.

Biogeochemical tags in fish: predicting spatial variations in strontium and manganese in Salmo trutta scales using stream water geochemistry

Fish scales of Salmo trutta exhibited regional patterning in Sr and Mn concentrations in major third-order tributaries in a small upland catchment (the Dee catchment in Wales, United Kingdom; drainage area ∼1800 km2) that appeared to reflect regional variability in catchment geology and stream water chemistry. When baseline signatures in scale element concentrations were established at a number of sites (n = 12) among the upper, middle, and lower regions of the Dee catchment, 73% of fish were classified to their region of capture based on Sr and Mn in scales. However, the regional patterning in scale chemistry was degraded when high-resolution catchment-wide variability in scale element concentrations was predicted using element concentrations in stream water as a proxy for Sr and Mn in scales at 792 sites in first-, second-, and third-order tributaries in the catchment (mean distance between neighbouring sites = 738 m, range = 41–3634 m). This analysis indicated that many locations throughout the catchment could be potential source locations and demonstrates that the initial classification accuracy was artificially inflated. We have illustrated limitations of the site-based study design commonly employed in biogeochemical tagging studies. Future studies should take account of potential variation in baseline signatures at fine geographical scales when determining the accuracy of stock discrimination using biogeochemical tags.

Ecological differentiation and local adaptation in two sister species of Neotropical Costus (Costaceae).

Reciprocal transplant experiments have often provided evidence of local adaptation in temperate plants, but few such studies have been conducted in the tropics. To enhance our knowledge of local adaptation in tropical plants, we studied natural populations of two recently diverged Neotropical plant species, Costus allenii and C. villosissimus, in central Panama. We found that these species display a parapatric distribution that reflects local environmental differences on a fine geographic scale: C. allenii is found along ravines in the understory of primary forest, while C. villosissimus is found along forest edges. Light availability was lower in C. allenii habitats, while precipitation and soil moisture were lower in C. villosissimus habitats. We carried out reciprocal transplant experiments with seeds and clones of mature plants to test the hypothesis that the parapatric distribution of these species is due to divergent adaptation to their local habitats. We found strong evidence of local adaptation, i.e., when grown in their "home" sites, each species outperformed the species from an "away" site. Our finding that C. allenii and C. villosissimus are mainly isolated by their microhabitats provides a first step toward understanding the mechanisms of adaptation and speciation in the tropics.

Spatial and temporal characteristics of insulator contaminations revealed by daily observations of equivalent salt deposit density.

The accurate estimation of deposits adhering on insulators is of great significance to prevent pollution flashovers which cause huge costs worldwide. Researchers have developed sensors using different technologies to monitor insulator contamination on a fine time scale. However, there is lack of analysis of these data to reveal spatial and temporal characteristics of insulator contamination, and as a result the scheduling of periodical maintenance of power facilities is highly dependent on personal experience. Owing to the deployment of novel sensors, daily Equivalent Salt Deposit Density (ESDD) observations of over two years were collected and analyzed for the first time. Results from 16 sites distributed in four regions of Hubei demonstrated that spatial heterogeneity can be seen at both the fine and coarse geographical scales, suggesting that current polluted area maps are necessary but are not sufficient conditions to guide the maintenance of power facilities. Both the local emission and the regional air pollution condition exert evident influences on deposit accumulation. A relationship between ESDD and PM10 was revealed by using regression analysis, proving that air pollution exerts influence on pollution accumulations on insulators. Moreover, the seasonality of ESDD was discovered for the first time by means of time series analysis, which could help engineers select appropriate times to clean the contamination. Besides, the trend component shows that the ESDD increases in a negative exponential fashion with the accumulation date (ESDD = a − b × exp(−time)) at a long time scale in real environments.

Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot.

BackgroundThe mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations.ResultsWe analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti.ConclusionsWe found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.

Temporal Population Genetic Structure of Yellow Perch Spawning Groups in the Lower Great Lakes

AbstractThis study tested the hypothesis that the genetic composition of Yellow Perch Perca flavescens spawning groups at specific sites remained consistent among years or age‐cohorts; this likely would influence spatial population structure and be important for delineating management units. Previous studies identified that spawning groups genetically differed among locations across fine geographic scales, but it was unknown whether these patterns persisted from year to year. We analyzed 15 nuclear DNA microsatellite loci from Yellow Perch spawning at six Lake Erie locations in 2009 in reference to two out‐groups spawning in Lakes St. Clair and Ontario. Results were compared with a prior study of samples from the same locations that had been collected in various years, ranging from 2001 to 2005. We evaluated consistency for two of the spawning groups across multiple birth‐year‐cohorts. Results indicated that the levels of genetic diversity were similar across all spawning groups and years. All eight spawning groups genetically differed from one other, with their allelic compositions varying between the two sampling periods. Some variation occurred among individual sampling years and birth‐cohorts, with the 2003 cohort being the most distinctive. Sampling groups contained relatively high proportions of full siblings (mean = 18.5%, ranging to 75% for the 2001 birth‐cohort spawning at the eastern Lake Erie site), yet inbreeding appeared relatively low. Differences at sampling sites over time did not appear to reflect genetic drift but may instead suggest that spawning groups reproduce in slightly different locations from year to year or perhaps within a given season; this merits examination. Spatial and temporal patterns may reflect kin‐group structuring and differential reproductive success, in which strong year‐classes dominate spawning groups and impact genetic structure.Received October 28, 2013; accepted October 22, 2014

Big Data and Big Cities: The Promises and Limitations of Improved Measures for Urban Life

New, data sources allow measurement of city characteristics and outcome variables higher frequencies and finer geographic scales than ever before. However, big data will not solve large urban social science questions on its own. Big data has the most value for the study of cities when it allows measurement of the previously opaque, or when it can be coupled with exogenous shocks to people or place. We describe a number of new urban data sources and illustrate how they can be used to improve the study and function of cities. We first show how Google Street View images can be used to predict income in New York City, suggesting that similar image data can be used to map wealth and poverty in previously unmeasured areas of the developing world. We then discuss how survey techniques can be improved to better measure willingness to pay for urban amenities. Finally, we explain how Internet data is being used to improve the quality of city services.

‘Southern’ Alternatives of Urban Diffusion: Investigating Settlement Characteristics and Socio‐Economic Patterns in Three Mediterranean Regions

AbstractThe present study investigates the relation between urban form and the socio‐economic patterns of the resident population in three southern European cities (Athens, Lisbon and Rome) featured by different processes of urban diffusion. The paper goes beyond the literature on sprawl focused on (residential, income and ethnic) segregation and the different features of the inhabitants of the suburbs and those of the inner cities residents. By integrating multivariate statistics and spatial analysis, a methodology is proposed, based on morphological and socio‐economic indicators available at a fine geographical scale. Results show how urban diffusion processes vary widely according to the context, as does the socio‐economic profile of the actors, stressing the need to think about different ‘southern European alternatives’ of sprawl.

The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae).

Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna.

There and back again: a review of residency and return migrations in sharks, with implications for population structure and management.

The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.