The city-fox phenomenon: genetic consequences of a recent colonization of urban habitat

The red fox (Vulpes vulpes) is one of the best-documented examples of a species that has successfully occupied cities and their suburbs during the last century. The city of Zurich (Switzerland) was colonized by red foxes 15 years ago and the number of recorded individuals has increased steadily since then. Here, we assessed the hypothesis that the fox population within the city of Zurich is isolated from adjacent rural fox populations against the alternative hypothesis that urban habitat acts as a constant sink for rural dispersers. We examined 11 microsatellite loci in 128 foxes from two urban areas, separated by the main river crossing the city, and three adjacent rural areas from the region of Zurich. Mean observed heterozygosity across individuals and the number of detected alleles were lower for foxes collected within the city as compared with their rural conspecifics. Genetic differentiation was significantly lower between rural than between rural and urban populations, and highest value of pairwise FST was recorded between the two urban areas. Our results indicate that the two urban areas were independently founded by a small number of individuals from adjacent rural areas resulting in genetic drift and genetic differentiation between rural and urban fox populations. Population admixture and immigration analysis revealed that urban-rural gene flow was higher than expected from FST statistics. In the five to seven generations since colonization, fox density has dramatically increased. Currently observed levels of migration between urban and rural populations will probably erode genetic differentiation over time.     

Macrogeographic and microgeographic genetic structure of the Chagas’ disease vector <Emphasis Type="Italic">Triatoma infestans</Emphasis> (Hemiptera: Reduviidae) from Catamarca,Argentina

The genetic structure in populations of the Chagas' disease vector Triatoma infestans from six localities belonging to areas under the same insecticide treatment conditions of Catamarca province (Argentina) was examined at macrogeographical and microgeographical scales. A total of 238 insects were typed for 10 polymorphic microsatellite loci. The average observed and expected heterozygosities ranged from 0.319 to 0.549 and from 0.389 to 0.689, respectively. The present results confirm that populations of T. infestans are highly structured. Spatial genetic structure was detectable at macrogeographical and microgeographical levels. Comparisons of the levels of genetic variability between two temporal samples were carried out to assess the impact of the insecticide treatment. The genetic diversity of the population was not significantly affected after insecticide use since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. However, loss of low frequency alleles and not previously found alleles were detected. The effective population size (N(e)) estimated was substantially lower in the second temporal sample than in the first; nevertheless, it is possible that the size of the remnant population after insecticide treatment was still large enough to retain the genetic diversity. Very few individuals did not belong to the local T. infestans populations as determined by assignment analyses, suggesting a low level of immigration in the population. The results of the assignment and first-generation migrant tests suggest male-biased dispersal at microgeographical level.     

Variation over space and time of Aedes aegypti in Phnom Penh (Cambodia): genetic structure and oral susceptibility to a dengue virus

We studied spatial and temporal variation in 20-23 Aedes aegypti samples collected in Phnom Penh and its suburbs to estimate the population genetic structure using allozymes and the susceptibility to a dengue-2 virus. Based on seven allozyme systems, we detected low levels of genetic exchanges (i.e. high, significant F(ST) values) between populations collected in the city centre, and different patterns of genetic structure for samples collected in the suburbs, depending on the type of environment and the date of collection. In the southern suburbs and the Chroy Chang Var Peninsula, differentiation became highly significant at the end of the dry season, whereas the opposite situation was observed for collections from the northern suburbs. Vector competence assessed by oral infections with a dengue-2 virus was lower for samples collected in the city centre than in the suburbs. A significant decrease of dengue susceptibility was observed in populations during the dry season. This study allows a model of Ae. aegypti population functioning in Phnom Penh to be suggested. Dynamics of dengue virus diffusion depend on the population genetic structure of the vector and its evolution over space and time.     

Genetic structure in urban and rural populations of Apodemus agrarius in Poland

The aims of this study were (i) to determine the genetic variability of the striped field mouse (Apodemus agrarius Pallas, 1771) population in the area of the Warsaw conurbation and the genetic differentiation among local populations of this species within the city, and (ii) to examine the influence of the degree of isolation on the appearance of such genetic structure. Comparison of the genetic structure of the urban population with that of populations inhabiting rural areas was intended to shed light on the depth of genetic changes in this species caused by life in an urban environment. Eight microsatellite loci were used for genotyping and these molecular analyses were successfully performed for 269 individuals. Genetic differentiation (F_ST) was much higher in the case of the urban population. STRUCTURE analysis indicated that this population was subdivided into several local populations, whereas for the rural locations, the highest likelihood was for a single genetic group (one genetically unstructured population). Moreover, in contrast to the rural population, we found no isolation by distance in the urban population. Despite clear subdivision of the urban population, the level of genetic variability was very similar in both analyzed groups. Our findings indicate the occurrence of an advanced process of differentiation of the urban population by microevolution, whereas populations from rural locations displayed very small and mainly insignificant genetic differentiation. Urban local populations, situated near the city borders or close to the natural ecological corridor (banks of the Vistula River), showed higher genetic variability and were less differentiated from populations inhabiting rural sites than from local populations in the city centre. These results provide support for the importance of ecological corridors in preserving the genetic variability of the urban striped field mouse population.     

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 humans 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 (Morogoro). 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 (2N_eM = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.     

Population genetic structure of the European kestrel Falco tinnunculus in Central Poland

We analysed the genetic structure of the European kestrel population of Central Poland using nine highly polymorphic microsatellite loci. Samples were collected in two urban locations (Warsaw and ?ód?) and two rural areas. Sampling locations were at nearly equal distances from each other along an east to west line. We performed genotyping in a total of 99 birds. The results revealed the presence of a genetic structure in the population investigated. Bayesian clustering indicated that samples originated from more than one population. Genetic differentiation was less pronounced among the birds nesting in Warsaw and in the two rural sites, whereas all pairwise comparisons with the ?ód? population indicated moderate and significant genetic differentiation. The observed pattern of differentiation might have been caused by two factors: changes in allele frequency between seasons and/or the founding of the urban population of ?ód? from a different source population than the urban population from Warsaw. Additionally, we found a rather high gene flow among kestrels from the Warsaw urban area and the two investigated rural areas.     

Analysis of the Alu insertion polymorphism in urban and rural populations of Siberia]

Polymorphic Alu-repeat loci of human genome are commonly used as effective genetic markers in population and evolution studies. In this work, the data on genetic structure of two Russian populations from Siberia obtained via analysis of five polymorphic Alu repeats are presented. The urban population was characterized by a slightly higher level of genetic diversity compared to the rural population. The value of genetic differentiation coefficient for the populations studied was 0.57%, pointing to the absence of genetic subdivision within the urban and rural populations. Phylogenetic analysis of these populations, together with literature data, shows that, with respect to the markers examined, the gene pool structure of Russian population is similar to that of other Caucasoid populations.     

How birds colonize cities: genetic evidence from a common waterbird,the Eurasian coot

Much effort has been devoted to identify ecological and life‐history traits which facilitate urban colonization by wild avian species, but surprisingly little is known about the population‐level mechanisms of urbanization processes. In general, two different patterns of urban colonization have been proposed: 1) the model of independent colonization predicts that birds colonize cities independently in different geographical regions; 2) the model of leapfrog colonization assumes a single colonization event, while additional urban populations are established from the initial urban populations. The aim of this paper was to determine the pattern of urban colonization in a common waterbird, the Eurasian coot Fulica atra. For this purpose, we analysed microsatellite variation in three pairs of urban and rural coot populations from central Poland. We found that a newly‐established urban population was genetically more similar to neighbouring rural populations than to long‐established urban populations, as indicated by the analysis of fixation index, genetic distance and Bayesian assignment of individuals to genetic clusters. These results are consistent with the model of independent colonization, where neighbouring rural populations are a source of individuals that colonize new urban areas. However, our analysis also showed significant differentiation between long‐established urban populations and adjacent rural populations, suggesting that genetic connectivity between two types of habitat decreases with increasing time since urbanization. Our study shows high complexity of urbanization processes in wild animal populations, as well as it underpins utility of molecular tools in studying population‐level mechanisms of urbanization.     

Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of F(ST) values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.     

Genetic structure of populations of Calomys laucha (muridae, sigmodontinae) from central Argentina

The genetic structure of populations of the Sigmodontinae rodent Calomys laucha was studied by means of allozyme electrophoresis. This highly opportunistic species is found preferably in periodically perturbed habitats of crop fields in central Argentina, where it can attain very high densities. A total of 17 enzymatic proteins assayed gave information on 25 loci; only four were monomorphic in the seven populations studied. Levels of genetic variability (H_o from 0.144 to 0.171; P_95% from 44% to 56%) were higher than mean values reported for mammals and rodents. These high levels of heterozygosity could be maintained by large populations that do not experience great fluctuations in size, or by a social structure consistent in many small breeding groups that are formed and dissappear every breeding season. Genetic differentiation at a macrogeographical scale (θ=0.018) was low but statistically significant, and showed no correlation with geographic distance between pairs of populations. The pattern of population differentiation found is compatible with a relatively recent range expansion.     

Microsatellite analysis of genetic structure in natural Triatoma infestans (Hemiptera: Reduviidae) populations from Argentina: its implication in assessing the effectiveness of Chagas' disease vector control programmes

The genetic structure in populations of the Chagas' disease vector Triatoma infestans was examined. Comparisons of the levels of genetic variability in populations of this species from areas with different periods since last insecticide treatment and from areas that never received treatment were also carried out. A total of 598 insects from 19 populations were typed for 10 polymorphic microsatellite loci. The average observed and expected heterozygosities ranged from 0.186 to 0.625 and from 0.173 to 0.787, respectively. Genetic drift and limited gene flow appear to have generated a substantial degree of genetic differentiation among the populations of T. infestans. Departures from Hardy-Weinberg expectations due to an excess of homozygotes suggested the presence of null alleles and population subdivision. Microgeographical analysis supports the existence of subdivision in T. infestans populations. Levels of genetic diversity in the majority of the populations of T. infestans from insecticide-treated localities were similar or higher than those detected in populations from areas without treatment. Since the populations of T. infestans are subdivided, a population bottleneck would result in independent genetic drift effects that could randomly preserve different combinations of alleles in each subpopulation. These events followed by a rapid population growth could have preserved high levels of genetic diversity. This study supports the hypothesis of vector population recovery from survivors of the insecticide-treated areas and therefore highlights the value of population genetic analyses in assessing the effectiveness of Chagas' disease vector control programmes.     

Isolation and characterization of microsatellite loci in the mosquito Anopheles stephensi Liston (Diptera: Culicidae)

The mosquito Anopheles stephensi is an important malaria vector in India, Pakistan, Iran and Afghanistan. Differences in egg morphology and chromosomal characters have been described between urban and rural forms of this mosquito but the population genetic structure remains unclear. In India this species is mainly urban, rural populations are largely zoophilic and not thought to transmit malaria. In eastern Afghanistan and the Punjab and Northwest Frontier Province, Pakistan, it is the major malaria vector. We have developed primers for 16 microsatellite loci to assist in defining the population structure and epidemiological importance of this mosquito.     

基于微卫星标记的印度中部Madhya Pradesh地区疟疾强化控制和非强化控制区的斯氏按蚊基因流和种群遗传结构分析（英文）

【目的】斯氏按蚊Anopheles stephensi是亚洲东南部城市人体疟疾的主要媒介,印度12%的疟疾病例由其引起。本实验研究了印度中部Madhya Pradesh地区东北部的疟疾强化控制(EMCP)区和非强化控制(非EMCP)区斯氏按蚊的基因流。在EMCP区,由于采用了各种疟疾防控措施因而疟疾病例首先降低,但是很快回升,说明总的疟疾风险维持稳定。【方法】应用7个微卫星位点,对印度中部Madhya Pradesh地区东北部的4个EMCP区和非EMCP区采集的斯氏按蚊进行基因分型,以分析各种群参数。【结果】发现各标记在所有种群中表现出高度的多态性。在两区间未发现很大的遗传多样性。观察到EMCP区的东部种群(FST=0.0485,RST=0.1112)比非EMCP区的北部种群(FST=0.020,RST=0.0145)具有较高的遗传分化,在EMCP区和非EMCP区之间观察到较高的基因流(12.90,6.16,5.06和2.38)。RST的灵敏度高于FST,说明分化可能是由于突变而非遗传漂变引起的。【结论】本研究表明,在EMCP区和非EMCP区内以及EMCP区和非EMCP区之间存在很高的基因流。基因流水平高以及抗虫性的发展似乎是EMCP区和非EMCP区疟疾病例发生增加的重要原因。     

Evidence of Habitat Structuring Aedes albopictus Populations in Réunion Island

Arbovirus vector dynamics and spread are influenced by climatic, environmental and geographic factors. Major Chikungunya and Dengue fever outbreaks occurring the last 10 years have coincided with the expansion of the mosquito vector Aedes albopictus to nearly all the continents. We characterized the ecological (larval development sites, population dynamics, insemination and daily survival rates) and genetic (diversity, gene flow, population structure) features of two Aedes albopictus populations from distinct environments (rural and urban) on Réunion Island, in the South-West Indian Ocean. Microsatellite analysis suggests population sub-structuring Ae. albopictus populations. Two genetic clusters were identified that were significantly linked to natural versus urban habitats with a mixed population in both areas. Ae. albopictus individuals prefer urban areas for mating and immature development, where hosts and containers that serve as larval development sites are readily available and support high population densities, whereas natural environments appear to serve as reservoirs for the mosquito.     

Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. In spite of geographical proximity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of isolation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation.     

Is urbanisation of European blackbirds (Turdus merula) associated with genetic differentiation?

Because of the extreme ecological and environmental changes along an urban–rural gradient, it has been proposed that urbanised and non-urbanised populations of the same species may be distinctly isolated. There is evidence that urban populations have become significantly different from the original forest populations in several aspects. However, little is known about the extent to which urban and non-urban populations are genetically isolated from each other. We tested the hypothesis of genetic differentiation by comparing the genomic DNA of an urban and a nearby forest-living European blackbird (Turdus merula) population. The present results suggest that, based on amplified fragment length polymorphism analysis, the urban population studied is very similar to a forest population at neutral genetic markers. Thus, despite indications of obvious functional genetic adaptation, the hypothesis of an overall genetic differentiation between our urban and forest populations could not be supported.Eberhard Gwinner died on 7 September 2004     

Epidemiology of monogenic hereditary diseases in Rostov oblast: Population dynamic factors determining the differentiation of the load of hereditary diseases in eight districts

A genetic epidemiological study has been carried out in eight raions (districts) of Rostov oblast (region) of Russia: Tsimlyansk, Volgodonskoi, Tselina, Egorlykskaya, Millerovo, Tarasovskaya, Rodionovo-Nesvetaiskaya, and Matveevo-Kurgan raions. The population structure (the parameters of the isolation by distance model, ethnic assortative marriage, random inbreeding (F _ST), endogamy index, and ie) and the genetic demographic characteristics of the regional population (vital statistics, Crow’s index, and its components) have been analyzed. The total sample size was 320 925 subjects (including 114 106 and 206 816 urban and rural residents, respectively). The load of the main types of Mendelian diseases (autosomal dominant (AD), autosomal recessive (AR), and X-linked diseases) has been calculated for the total sample from eight districts and separately for the urban and rural populations. Substantial differences between individual districts in the AD and AR genetic loads have been found, especially upon separation into urban and rural samples. The results of correlation analysis suggest that migration and genetic drift are the main factors of genetic differentiation of populations with respect to the prevalence of hereditary diseases.     

Independent colonization of multiple urban centres by a formerly forest specialist bird species

Urban areas are expanding rapidly, but a few native species have successfully colonized them. The processes underlying such colonization events are poorly understood. Using the blackbird Turdus merula, a former forest specialist that is now one of the most common urban birds in its range, we provide the first assessment of two contrasting urban colonization models. First, that urbanization occurred independently. Second, that following initial urbanization, urban-adapted individuals colonized other urban areas in a leapfrog manner. Previous analyses of spatial patterns in the timing of blackbird urbanization, and experimental introductions of urban and rural blackbirds to uncolonized cities, suggest that the leapfrog model is likely to apply. We found that, across the western Palaearctic, urban blackbird populations contain less genetic diversity than rural ones, urban populations are more strongly differentiated from each other than from rural populations and assignment tests support a rural source population for most urban individuals. In combination, these results provide much stronger support for the independent urbanization model than the leapfrog one. If the former model predominates, colonization of multiple urban centres will be particularly difficult when urbanization requires genetic adaptations, having implications for urban species diversity.     

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual‐based sampling across an urban‐rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban‐rural landscape. We assessed functional connectivity by applying an individual‐based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector‐based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built‐up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man‐made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.     

Microsatellite variation in Daphnia pulex from both sides of the Baltic Sea

Despite large genetic differentiation among neighbouring populations of many freshwater zooplankton species, a macrogeographical homogeneity of allozyme variation is generally observed. A study on breeding systems in Scandinavian populations of Daphnia pulex suggested a latitudinally related cline in breeding system with both diploid cyclic parthenogens and diploid obligate parthenogens at the latitude of 60-61 degrees N. Variation at neutral markers may be more affected by selection at linked loci in such species than in strictly sexual species. In this paper I present a study of variation at five microsatellite loci in a total of 34 populations from small ponds and rockpools on both sides of the Baltic Sea at 60-61 degrees N. Two major groups, which may represent different species of the D. pulex complex, are defined with the microsatellites. Neighbouring populations show both similar and well differentiated genetic composition. Populations separated by larger geographical distances show only a large differentiation and a macrogeographic pattern. The large differentiation observed at small distances can be explained with small effective population size: variation at the microsatellite loci has been shaped by population bottlenecks followed with expansion in size, and possibly by selection. No conclusive evidence is found for obligative parthenogenesis.