Genetic diversity and structure of urban populations of Pieris butterflies assessed using amplified fragment length polymorphism

Conservation programs in urban ecosystems need to determine the genetic background in populations of urban dwellers. We examined the genetic diversity and structure of Pieris rapae and P. melete using AFLP markers, and compared them between species and between urban and rural environments. As a result: (i). in both species, there was no reduction in genetic diversity within urban populations by direct comparison of diversity measurements, although the analysis of molecular variance suggested significant reductions in the variance within seasonal subpopulations in urban populations; (ii). P. rapae retained greater genetic diversity within species and populations; (iii). populations of both species showed significant genetic differentiation, and P. melete was more strongly subdivided; (iv). in both species, geographically close populations did not cluster with one another in the upgma analysis; (v). there was no genetic isolation due to geographical distance in either species; (vi). the genetic composition of seasonal subpopulations differed in urban populations of both species, and the genetic distances among subpopulations were correlated with seasonal differences in P. rapae and with temporal differences in P. melete. These results indicate that the genetic diversity in urban populations of both species was reduced at times, but was maintained by dispersal from genetically differentiated populations. Differences in the ability and mode of dispersal in the two species may be reflected in the degree of population subdivision and patterns of seasonal change in the genetic composition.     

A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations

Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.     

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.     

Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation

Once widely distributed throughout Africa, cheetahs (Acinonyx jubatus) occur today within fragmented populations and are listed as vulnerable by the IUCN. Botswana currently hosts the second largest cheetah population throughout the species’ range. This study initiated a molecular genetic survey of wild Botswana cheetah populations. It focused on the relatedness within presumed social groups using 14 microsatellite markers and revealed a higher proportion of unrelated male coalitions than was expected. Based on the unrelated cheetahs only, the estimation of the genetic variation corresponded with results from recent studies on different African populations. The analysis of unrelated individuals indicated limited genetic differentiation between cheetahs from different regions of Botswana. This suggests that the Botswana cheetah population might represent a unique panmictic population as long as sufficient levels of gene flow are maintained within the distribution range. This baseline information will now be incorporated to develop management strategies and set priorities for cheetah conservation in Botswana.     

High interpopulation homogeneity in Central Argentina as assessed by Ancestry Informative Markers (AIMs)

The population of Argentina has already been studied with regard to several genetic markers, but much more data are needed for the appropriate definition of its genetic profile. This study aimed at investigating the admixture patterns and genetic structure in Central Argentina, using biparental markers and comparing the results with those previously obtained by us with mitochondrial DNA (mtDNA) in the same samples. A total of 521 healthy unrelated individuals living in 13 villages of the Córdoba and San Luis provinces were tested. The individuals were genotyped for ten autosomal ancestry informative markers (AIMs). Allele frequencies were compared with those of African, European and Native American populations, chosen to represent parental contributions. The AIM estimates indicated a greater influence of the Native American ancestry as compared to previous studies in the same or other Argentinean regions, but smaller than that observed with the mtDNA tests. These differences can be explained, respectively, by different genetic contributions between rural and urban areas, and asymmetric gene flow occurred in the past. But a most unexpected finding was the marked interpopulation genetic homogeneity found in villages located in diverse geographic environments across a wide territory, suggesting considerable gene flow.     

Genome-wide SNP typing reveals signatures of population history

Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23-31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities.     

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high‐resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)‐based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine‐scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (F_ST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late‐maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.     

Integrative approach revealed contrasting pattern of spatial structuring within urban and rural biotypes of Culex pipiens

Population structure of pests is an important issue when designing management strategies to optimize control measures. In this study, we investigated a spatial pattern of genetic and phenotypic variation within seven urban and within six rural populations of Culex pipiens from Vojvodina Province (Serbia) incorporating landscape genetic methods (using allozyme data) and wing size and shape (using geometric morphometric approach). Comparing rural samples, no strong genetic groupings of individuals were detected. Nevertheless, traditional approaches where individuals are pre‐assigned to populations, including F statistics and amova (analysis of molecular variance), revealed low, but significant genetic differentiation among samples. Similarly, phenotypic data (wing size and shape) indicated some level of heterogeneity among rural samples. Contrary to genetic homogeneity found within rural biotype, the individual‐based structuring characterized urban biotype. Geneland revealed the presence of two genetic clusters within urban group which is in concordance with F_ST and amova results. These results showed that sample from Novi Sad (NS) is a distinct genetic unit, which has been likely resulted in intensive insecticide use over several decades. Furthermore, phenotypic differentiation supported the existence of spatial structuring. Therefore, complementary use of molecular markers and phenotypic traits may be a powerful tool for revealing hidden spatial diversity within Cx. pipiens.     

Continent‐wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator,the spruce budworm (Choristoneura fumiferana)

The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba–Ontario border), and Eastern (Manitoba–Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co‐adapted blocks of genes, and gene flow between subpopulations.     

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.     

Genetic differentiation within and between populations of a hermaphroditic freshwater planarian

Dispersal of individuals is an important factor that can influence genetic differentiation between populations. The hermaphroditic freshwater planarian Schmidtea polychroainhabits shallow regions of lakes and streams, in which they appear to be continuously distributed. In the present study we used three highly polymorphic markers for analysing small-scale and large-scale genetic structure within one, and between four natural lake populations. Genetic differentiation could already be observed between samples collected at least 13 m apart, but not between neighbouring samples, and was most pronounced between samples from different lakes. Probably due to the high variance in F(ST)values, a significant correlation between genetic differentiation and geographic distance could not be observed. These results show that individual dispersal of S. polychroa is limited, but that there is gene flow between subpopulations from the same lake. They further suggest that long-distance dispersal and gene flow between lakes, if present, is not a common process in S. polychroa.     

VNTR loci reveal differentiation between and structure within populations of the eastern barred bandicoot Perameles gunnii

The Eastern Barred Bandicoot Perameles gunnii has declined in abundance within mainland south-eastern Australia, to a relict wild population of less than 100 individuals in Hamilton, Victoria. It is more common, but is also declining in Tasmania. Genomic DN A variability was compared within and between surviving populations of P. gunnii using variable number of tandem repeat (VNTR) markers in one of two ways. First, average percentage differences (APDs) were determined between profiles for two VNTR probe—endonuclease combinations. Secondly, because one of these combinations revealed two multiallelic VNTR loci, genotypes were assigned and analysed for homogeneity of allele frequencies among subpopulations, for deviation of heterozygosity from Hardy-Weinberg equilibrium within populations and for genetic structuring among individuals from different subpopulations. The results of both the APD and defined locus approaches showed consistent trends within and between populations. Genetic variability was higher among mainland P. gunnii than in Tasmanian populations (higher APDs, number of alleles, and heterozygosity at one locus), despite the known decline and subdivision of the Hamilton population. Eleven per cent of the variability detected in Hamilton was attributed to genetic differentiation between east and west subdivisions of the population. Departure from random mating indicating local inbreeding within collecting localities was evident for one locus in both north and south Tasmania, particularly at one locality. AH alleles at both loci were unique to either Hamilton or Tasmanian P. gunnii. The initial captive colony contains high heterozygosity for these loci. It is concluded that VNTR markers can be of benefit for use in studies of population differentiation and for conservation management.     

Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers. A Bayesian structure analysis identified two subpopulations, which were confirmed by principal coordinate analysis (PCoA). One subpopulation consisted mainly of genotypes originating from the UK, while germplasm mostly from Continental Europe was grouped into the second subpopulation. LD (r²) decay was rapid and occurred within 0.4 cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6 cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials of perennial ryegrass. However, different strategies need to be applied depending on the material used. Genome-wide association study (GWAS) with several hundred markers can be applied within synthetic varieties to identify large (up to 10 cM) genomic regions affecting trait variation. A combination of available and novel DNA markers is needed to achieve resolution required for GWAS in elite breeding materials. An even higher marker density of several million SNPs might be needed for GWAS in diverse ecotype collections, potentially resulting in quantitative trait polymorphism (QTP) identification.     

Linkage disequilibrium between microsatellite markers in the Swedish Sami relative to a worldwide selection of populations

The pattern of linkage disequilibrium (LD) is affected by a number of factors, including population demography. High LD is seen in populations with a relatively limited and constant size, presumably because of genetic drift. We have examined the extent of LD among over 300 genome-wide pattern microsatellite loci in 29 populations from around the world. The pattern of LD varied between populations, with a larger extent of LD in populations with limited size relative to larger populations. In addition, the LD between 88 less well-spaced microsatellite markers from 10 different genomic regions was examined in the Sami compared with the general Swedish population. For these markers, increased LD extending up to 5 Mb was detected in the Sami. The amount of LD also differed between the chromosomal regions. The amount of LD in the Sami makes this population suitable for the mapping of complex genetic traits.Åsa Johansson, Veronika Vavruch-Nilsson contributed equally to the report     

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.     

Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi‐allelic LD, D′, and χ^′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross‐sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.     

Population genetic structure of a widespread coniferous tree, Taxodium distichum [L.] Rich. (Cupressaceae), in the Mississippi River Alluvial Valley and Florida

Studies of genetic variation can elucidate the structure of present and past populations as well as the genetic basis of the phenotypic variability of species. Taxodium distichum is a coniferous tree dominant in lowland river flood plains and swamps of the southeastern USA which exhibits morphological variability and adaption to stressful habitats. This study provides a survey of the Mississippi River Alluvial Valley (MAV) and Florida to elucidate their population structure and the extent of genetic differentiation between the two regions and sympatric varieties, including bald cypress (var. distichum) and pond cypress (var. imbricatum). We determined the genotypes of 12 simple sequence repeat loci totaling 444 adult individuals from 18 natural populations. Bayesian clustering analysis revealed high levels of differentiation between the MAV and the Florida regions. Within the MAV region, there was a significant correlation between genetic and geographical distances. In addition, we found that there was almost no genetic differentiation between the varieties. Most genetic variation was found within individuals (76.73?%), 1.67?% among individuals within population, 15.36?% among populations within the regions, and 9.23?% between regions within the variety. Our results suggest that (1) the populations of the MAV and the Florida regions are divided into two major genetic groups, which might originate from different glacial refugia, and (2) the patterns of genetic differentiation and phenotypic differentiation were not parallel in this species.     

The effect of urbanisation on avian morphology and latitudinal gradients in body size

Urban areas occupy a large and growing proportion of the earth. Such sites exhibit distinctive characteristics relative to adjacent rural habitats, and many species have colonised and now successfully exploit urban habitats. The change in selection pressures as a result of urbanisation has led to trait divergence in some urban populations relative to their rural counterparts, but studies have generally been local in scale and the generality of differentiation thus remains unknown. The European blackbird Turdus merula is one of the commonest urban bird species in the Western Palearctic, but populations vary substantially in the length of time they have been urbanised. Here we investigate patterns of morphological variation in European blackbirds occupying 11 paired urban and rural habitats across much of the urbanised range of this species and spanning 25° of latitude. First, we assessed the extent to which urban and rural blackbirds are differentiated morphologically and the consistency of any differentiation across the range. Paired urban and rural Blackbird populations frequently exhibited significant morphological differences, but the magnitude and direction of differentiation was site dependent. We then investigated whether the nature of latitudinal gradients in body‐size differed between urban and rural populations, as predicted by differences in the climatic regimes of urban and rural areas. Blackbird body‐size exhibited strong latitudinal gradients, but their form did not differ significantly between urban and rural habitats. The latitudinal gradient in body size may be a consequence of Seebohm's rule, that more migratory populations occurring at high latitudes have longer wings. We conclude that while there can be substantial morphological variation between adjacent urban and rural bird populations, such differentiation may not apply across a species’ range. Locality specific differentiation of urban and rural blackbirds may arise if the selection pressures acting on blackbird morphology vary in an inconsistent manner between urban and rural habitats. Alternatively, phenotypic divergence could arise in a stochastic manner depending on the morphological traits of colonists, through founder effects.     

Genetic variability, body characteristics and reproductive parameters of neighbouring rural and urban common kestrel (Falco tinnuculus) populations

We tested the genetic and ecological differences between neighbouring urban and rural populations of common kestrels (Falco tinnuculus) in southern Bohemia. The aims were to (1) assess the genetic variability of the studied kestrel populations using microsatellite markers, (2) check the genetic relatedness of individuals within the urbanization gradient, and (3) compare possible gradients of body characteristics and reproductive parameters on the urbanization gradient. The mean expected allelic polymorphism did not differ among the studied populations, which were not genetically separated (F _ST  = 0.0003, P = 0.781). Also, an individual assignment test did not show a separation of these populations. Urban kestrels that bred in the city centre were indicatively more related than others, and no relationship was found in the rural kestrel population. Kestrel females were heavier towards the city centre, but males did not show this relationship. Nest distance from the city centre had no significant effect on any of the tested reproductive parameters. Our results do not support the notion of genetic differentiation between rural and urban kestrels, but revealed trends in body characteristics and genetic relatedness along the urbanization gradient.     

High Differentiation among Eight Villages in a Secluded Area of Sardinia Revealed by Genome-Wide High Density SNPs Analysis

To better design association studies for complex traits in isolated populations it''s important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates.