Geographic structuring of molecular and morphological polymorphism in Pyrenean populations of the snail Cepaea nemoralis

To determine whether geographic patterns of variation in the frequency of shell polymorphisms in the land snail Cepaea nemoralis mark regions of extensive genetic differentiation, allele frequencies at six polymorphic enzyme-encoding loci were analyzed electrophoretically in 74 samples from the central part of the Spanish Pyrenees. Within a large area effect for unbanded shells on the southern slope of the Pyrenees, there is no enzyme locus at which allele frequencies are homogeneous. Because this morphological area effect does not mark a region of pervasive genetic change, the genetic structure of populations in the region studied does not conform to recent models of area effect speciation. Factor analysis of allele frequencies at three loci controlling shell polymorphisms and six enzyme loci separated populations on the southern slope into two groups, one of which is similar to the group of populations on the northern slope. There is therefore considerable geographic structuring of both molecular and morphological polymorphism in this species.     

Interaction between area effects and variation with habitat in Cepaea

Populations of Cepaea nemoralis in Warwickshire occupy habitats of considerable temporal stability, most being at least 250 years old, and some much older. As expected from earlier work, shell pattern polymorphisms in these populations show variation with habitat of a kind suggesting the operation of visual selection for crypsis. They also show patterns of microgeographical variation unrelated to habitat. Although of a less extreme character, this variation resembles the 'area effects' seen in downland populations of Cepaea , in the lack of coincidence of variation at different loci, and in the existence of stronger and larger scale patterns in banding than in colour morphs. A similar explanation is advanced for their occurrence: previous bottlenecks and colonization from small relicts with founder effects. The less marked character of the variation is expected from the greater habitat stability and continuity in Warwickshire compared with downland. A clear colonization effect is seen in the inverse relationship between age of habitat and frequency of yellow in woodland populations. The results suggest that population histories affect variation in Cepaea even in areas of relative habitat stability.     

Gene frequencies, genetic background and environment in Pyrenean populations of Cepaea nemoralis (L.)

Microgeographical genetic differentiation of populations of the polymorphic land snail Cepaea nemoralis (L.) has been the subject of intensive investigation. The importance of environmental selection acting at the loci which control the shell polymorphism in determining the distribution of genes in this species remains a matter of considerable controversy. Some populations of C. nemoralis in the central Pyrenees show striking local associations of morph frequency (and particularly of the frequency of unhanded shells) with topography which have been ascribed to the action of natural selection.
In the Ter valley (eastern Spanish Pyrenees) populations described here, however, the pattern of association of the frequencies of the shell morphs with topography is quite different from that found in the central Pyrenees. In particular, the distribution of unhanded shells is almost the inverse of that found in some previously studied populations. The general picture of variation in relation to topography in Pyrenean C. nemoralis populations is now seen to be one of great local consistency within valley systems, but of considerable differences between valley systems. This variation in population structure may be due either to cryptic and undetected environmental differences between valley systems or to evolutionary divergence between their C. nemoralis populations. The difficulty of deciding between these two conflicting hypotheses emphasizes the limitations of the technique of simply examining the distribution of individual genes in natural populations as a method of analysing their evolutionary history.     

History or current selection? A molecular analysis of 'area effects' in the land snail Cepaea nemoralis.

We have used molecular variation in microsatellite and mitochondrial DNA to throw light on the origins of enigmatic geographical patterns, known as 'area effects', in the shell polymorphisms of the land snail Cepaea nemoralis. Our aim was to assess the relative importance of recent selection and historical events in the formation of these patterns. On the Marlborough Downs in Wiltshire, England, the 'type locality' for area effects, the frequencies of microsatellites are significantly associated with the frequencies of alleles for shell banding. A less clear association is found between microsatellites and shell colour. Mitochondrial haplotypes show no significant relationships. Although the correlated geographical patterns could be the results of random genetic drift from an initially uniform array of populations, the magnitudes of the patterns, and of the correlations between them, seem too strong to have arisen by drift since the last glaciation. Our results suggest that invasions from refugia have been the most important factors in forming area effects.     

Contrasting patterns of variation in urban populations of Cepaea (Gastropoda: Pulmonata): a tale of two cities

The shell colour and banding polymorphisms in urban populations of Cepaea snails were studied in Sheffield (England) and Wrocław (Poland), which are two cities of similar size. Both Cepaea nemoralis and Cepaea hortensis were found in Sheffield, but only C. nemoralis was found in Wrocław. In neither city was variation with habitat apparent, nor was there evidence of large-scale geographical patterns. Spatial autocorrelation analyses revealed only vaguely defined local clusters. There was a greater degree of among-population variation in Sheffield, and more cases of extreme frequencies and low levels of polymorphism. Wrocław populations were more uniform and highly polymorphic. These differences can be related to the history of these snails in each city. Sheffield has been colonized mainly in the last 20 years, and some parts of the city with apparently suitable habitat remain unoccupied. Leptokurtic dispersal of small propagules followed by local spread appears likely. Values of F _ST resemble those seen in districts elsewhere with 'Area Effects'. Although there are ancient woodlands within the city, they have been colonized too recently for selection to achieve a new balance. Wrocław has held Cepaea populations for at least 100 years, and they are denser and more continuous. Shaded habitats are recent and temporary; the overall pattern of variation matches that seen in open habitats in districts elsewhere in which variation with habitat is apparent, and values of F _ST also correspond. Population history and the character of dispersal clearly affect the patterns of variation observed.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 27–39.     

Cepaea on Salisbury Plain: patterns of variation, landscape history and habitat stability

Patterns of variation in Cepaea nemoralis and C. hortensis on Salisbury Plain are related to its landscape history. Areas of arable or mixed farming, with hedgerows and woods, show patterns of variation with habitat and topography. Areas of downland, until recently heavily grazed by sheep, show area effects. Cepaea populations in these downland areas would have been much rarer, and more isolated when grazing was intense. This pattern is repeated in other parts of southern England, showing that area effects in Cepaea are strongly associated with areas of habitat instability, where Cepaea survived as small and isolated populations until recently. This evidence enhances the plausibility of explanations of area effects involving isolation, founder effect or local selection, and co-adaptation.     

Differentiation among populations with migration, mutation, and drift: implications for genetic inference

Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hierarchically structured populations subject to migration, mutation, and drift. In addition to the expected correlation in allele frequencies among populations in the same geographic region, we demonstrate that there is a substantial correlation in allele frequencies among regions at the top level of the hierarchy. We propose a hierarchical Bayesian model for inference of Wright's F-statistics in a two-level hierarchy in which we estimate the among-region correlation in allele frequencies by substituting replication across loci for replication across time. We illustrate the approach through an analysis of human microsatellite data, and we show that approaches ignoring the among-region correlation in allele frequencies underestimate the amount of genetic differentiation among major geographic population groups by approximately 30%. Finally, we discuss the implications of these results for the use and interpretation of F-statistics in evolutionary studies.     

The distribution and variation of three species of land snail near Rickmansworth, Hertfordshire

The distribution of Arianta arbustorum, Cepaea nemoralis and C. hortensis , and the variations in the shell polymorphism of the Cepaea species have been studied in an area of low chalk downland and alluvial river valleys near Rickmansworth, Hertfordshire. The distribution of A. arbustorum is restricted, the species being largely confined to the bottoms of river valleys, especially in hedgerows. Variations in dampness seem the most likely limiting factor. C. hortensis is widespread and found in many habitats, but C. nemoralis is largely confined to woods, and is especially common in beechwoods. The morph-frequencies of C. nemoralis and C. hortensis vary in such a way as to suggest the operation of climatic and visual selection. In C. hortensis there are area effects for the presence or absence of pink five-banded shells, and there is an overall linkage disequilibrium resulting in an excess of unbandeds in non-yellow shells. Reasonable evidence for the operation of random factors in determining the morph-frequencies of populations of Cepaea in the area has been found only for three very disturbed populations. It is suggested that the large number of selective forces known to act on Cepaea populations in this area will account for the variation in morph-frequencies in populations from the same area or habitat.     

GENETIC DIVERSITY AND POPULATION STRUCTURE IN CAMELLIA JAPONICA L. (THEACEAE)

Camellia japonica is a widespread and morphologically diverse tree native to parts of Japan and adjacent islands. Starch gel electrophoresis was used to score allelic variation at 20 loci in seeds collected from 60 populations distributed throughout the species range. In comparison with other plant species, the level of genetic diversity within C. japonica populations is very high: 66.2% of loci were polymorphic on average per population, with a mean number of 2.16 alleles per locus; the mean observed and panmictic heterozygosities were 0.230 and 0.265, respectively. Genotypic proportions at most loci in most populations fit Hardy-Weinberg expectations. However, small heterozygote deficiencies were commonly observed (mean population fixation index = 0.129). It is suggested that the most likely cause of the observed deficiencies is population subdivision into genetically divergent subpopulations. The overall level of population differentiation is greater than is typically observed in out-breeders: The mean genetic distance and identity (Nei's D and I) between pairs of populations were 0.073 and 0.930, respectively, and Wright's Fst was 0.144. Differences among populations appeared to be manifested as variation in gene frequencies at many loci rather than variation in allelic composition per se. However, the patterns of variation were not random. Reciprocal clinal variation of gene frequencies was observed for allele pairs at six loci. In addition, principal components analysis revealed that populations tended to genetically cluster into four regions representing the geographic areas Kyushu, Shikoku, western Honshu, and eastern Honshu. There was a significant relationship between genetic and geographic distance (r = 0.61; P < 0.01). Analysis of variance on allozyme frequencies showed that there was approximately four times as much differentiation among populations within regions, as among regions. It is likely that the observed patterns of population relationships result from the balance between genetic drift in small subpopulations and gene flow between them.     

The karyotype of Cepaea sylvatica (Pulmonata: Helicidae) and its relationship to those of C. hortensis and C. nemoralis

The karyotypes of Cepaea nemoralis (L.) and C. hortensis (Müller), with 2n=44 and a conspicuously large pair of chromosomes, are described and compared with that of C. sylvatica (Draparnaud) which has 2n=50. The karyotype of C. sylvatica also has a conspicuously large pair of chromosomes but the comparison suggests that these have an independent origin from those in the 2n = 44 species. There is no evidence that the large chromosomes in C. nemoralis and C. hortensis have originated from simple fusion of chromosomes from a 2n=50 karyotype with chromosomes all sub-equal such as is reported for C. vindobonensis. It may be that such a karyotype with little size differentiation amongst the chromosomes is not a primitive feature in the Helicinae. The relationship of shell colour and banding polymorphism to the chromosome architecture is discussed.     

Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow) was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate.     

The habitats of the land snail Cepaea nemoralis (L.) on downland and their ecogenetie significance

Population densities of adult Cepaea nemoralis (L.) were estimated for nine chalk grassland sites on the South Downs. Estimates of cover, species composition and height of vegetation were also obtained. The density of C. nemoralis was positively associated with Bromus erectus cover, and negatively with Festuca spp. cover. This finding, confirmed by an earlier survey, suggests that the density of C. nemoralis in chalk grassland is directly or indirectly governed by mammalian grazing pressure, and not by the availability of suitable food. Intensely grazed downland is an unsuitable, or at best a marginal habitat for C. nemoralis. This conclusion is discussed with particular reference to 'area effects' in the shell character polymorphism, often found in downland populations of C. nemoralis.     

Gene frequency changes in Cepaea snails on the Marlborough Downs over 25 years

In 1985 we resurveyed the sites on the Marlborough Downs in southern England at which Cain and Currey in 1960/61 sampled Cepaea snails and thence introduced the term 'area effects' to describe large areas of uniform morph frequency. Some sites no longer harboured Cepaea and at others the species composition had changed, with a general spread of Cepaea hortensis at the expense of Cepaea nemoralis. The majority, however, permitted comparison of morph frequencies between the two surveys. In C. nemoralis, we detected a significant overall decrease in the frequency of the brown morph and estimate selection as 5–9% per generation. There was no apparent change in frequencies of banded morphs. In C. hortensis we detected a significant overall increase in the frequency of unbanded shells (1–3% selection per generation) and an almost significant decrease in the frequency of fusions within the banded class. There was insufficient colour polymorphism in C. hortensis to allow analysis of colour morph frequencies. These changes—all in the direction of reduced absorption of solar energy—resemble others detected in both species at other localities in southern England. Possible explanations include large-scale climatic effects and changes in vegetation.     

HLA-DR polymorphism in a Senegalese Mandenka population: DNA oligotyping and population genetics of DRB1 specificities.

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1*1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequent specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52b (DRB3*02) represents as much as 80.7% of all DR52 haplotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the Mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes.     

NONSTATIONARY PATTERNS OF ISOLATION‐BY‐DISTANCE: INFERRING MEASURES OF LOCAL GENETIC DIFFERENTIATION WITH BAYESIAN KRIGING

Patterns of isolation‐by‐distance (IBD) arise when population differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which genetic differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species.     

Variation in body colour in western Irish populations of Cepaea nemoralis (L.)

Samples of Cepaea nemoralis (L.) taken from sand-dune, lowland and mountain populations show differences in body colour. Overall, sand-dune populations are much paler than those in the other two areas. On sand-dunes, darker and more variable populations are found in densely vegetated habitats; in the lowland, darker forms occur further inland but there is no correlation with vegetation; mountain populations are darker and less variable on north- than south-facing slopes. Overall differences between areas can be ascribed to climatic selection and differences in variation within areas to niche width.     

Disequilibrium in some Cepaea populations

Phenotypic disequilibrium is a measure available, along with morph frequency, in many published sets of sample data recording the polymorphism of shell colour and pattern in the snail Cepaea nemoralis. The relation of disequilibrium to morph frequency for the colour (pink/yellow) and banding (unbanded/banded) loci has been examined for a large and widespread set of data. The direction of disequilibrium is a function of frequency at the two loci in a way that suggests that selection favours combinations of common morphs, whichever they are. This could indicate that such combinations are common because they have been selected. The data are therefore consistent with the proposal that populations are generally subject to selection of varying directions at different places and times, acting on the phenotype. In combination with migration, such selection could lead to prolonged polymorphism.     

Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.     

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.     

黑头酸臭蚁微卫星标记的分离与开发(英文)

【目的】本研究旨在分离黑头酸臭蚁Tapinoma melanocephalum基因组微卫星标记,确定这些微卫星位点的多态性。【方法】使用454 GS-FLX焦磷酸测序技术开发来自中国华南陆地和岛屿的11个黑头酸臭蚁地理种群基因组微卫星位点。从随机设计的100对微卫星引物中筛选出10对引物,用于确定黑头酸臭蚁4个地理种群［东澳岛(DAD)、荷包岛(HBD)、梅州(MZ)和山咀(SJ)］10个微卫星位点的多态性,分析种群遗传多样性和种群分化。【结果】从11个黑头酸臭蚁地理种群基因组中成功开发和分离10对微卫星引物。在DAD, HBD, MZ和SJ 4个地理种群中,10个微卫星位点中7个有高多态性,这10个位点均显著偏离Hardy-Weinberg平衡;每个位点的等位基因数量(A)是3.50~9.00个,每个地理种群每个位点等位基因丰富度(A_R)在1.992~12.938之间。岛屿地理种群(DAD和HBD)的AR和预期杂合度(H_E)与大陆地理种群(MZ和SJ)的相比差异不显著。4个地理种群均显示高水平遗传分化(F_ST=0.15969);HBD和MZ种群与其他配对地理种群相比,遗传分化较高(F_ST=0.185),基因流较低,说明这两个种群基因流被限制。此外,遗传变异来自种群内个体之间。【结论】筛选新的微卫星位点能够为研究黑头酸臭蚁种群结构和繁殖结构提供有效工具,以深入了解其传播机制。