水杉孑遗居群AFLP遗传变异的空间分布

本研究采用空间自相关分析方法对水杉 (Metasequoiaglyptostroboides)孑遗居群AFLP遗传变异的空间结构进行了研究 ,以探讨水杉孑遗居群遗传变异的分布特征及其形成机制。根据 6对AFLP选择性引物扩增的 46个多态性位点 ,选择了其表型频率在 2 5 %～ 75 %的 2 7个AFLP标记 ,运用等样本频率方法和等地理距离间隔方法分别对 3 9株和 3 7株原生母树进行了空间自相关系数Moran’sI值计算。结果表明 :水杉孑遗居群缺乏空间结构 ,绝大多数AFLP位点变异为随机分布的空间模式 ,但也有少数位点存在显著性随机相关 ,在 4～ 8km地理距离间隔显示负相关 ,说明该间隔可能是水杉孑遗居群的部分基因交流的有效屏障。水杉原生母树分布存在 12～ 2 8km的明显距离间隔空挡 ,说明人类从迁入该区域起就影响着水杉孑遗居群的原始生境 ,导致其生境片断化、景观破碎 ,进而形成岛屿状分布格局 ,并引起了水杉残留居群的随机遗传漂变。根据本研究结果 ,结合水杉孑遗居群较低的遗传多样性 ,分析探讨了水杉孑遗居群濒危的机理 ,并提出了相应的保育策略 ,为水杉的有效保育提供了科学依据     

濒危物种--巴东木莲等位酶遗传变异的空间自相关分析

采用空间自相关分析方法对巴东木莲目前残留的两个最大居群, 小溪居群的40个个体和桑植居群的28个个体等位酶遗传变异的空间结构进行了研究, 以揭示两居群遗传变异的空间模式, 并探讨其形成机制及与巴东木莲致濒原因、过程之间的关系。根据检测出来的8个酶系统的19个酶位点, 选择基因频率大于0 1小于0 9的等位基因, 运用等样本频率和等地理距离间隔两种方法分别计算两居群不同距离等级下的Moran’sI空间自相关系数。结果表明: 小尺度的小溪居群等位基因的遗传变异缺乏空间结构, 为随机分布模式。巴东木莲生境片断化的桑植居群则是相反的结果, 遗传变异存在明显的空间结构, 遗传变异空间分布为斑块状。造成这种差别的原因可能是桑植居群片断化和地理隔离造成的基因流的限制。上述结果为进一步制定有效的巴东木莲的保育措施提供科学的理论依据。     

Fine-scale spatial genetic structure of an endangered marsh herb, Caldesia grandis (Alismataceae)

The endangered marsh herb, Caldesia grandis, is native to China. We investigated the spatial structure of the genetic variation of three populations of C. grandis using RAPD markers and spatial autocorrelation analysis, based on the method of equal distance interval. A total of 157 individuals were sampled from four patches collected from the region of Hunan and Yunnan Provinces, China. Among the polymorphic bands generated by seven selective primers, polymorphic bands with frequencies ranging from 20 to 80% were used to calculate Moran's I spatial autocorrelation coefficient for each patch. We found significant spatial structure of genetic variation in the three patches in Bei Hai (BH) (patches BH-1 and BH-2) and Guai Hu (GH) (patch GH-1) populations of C. grandis (with significant positive autocorrelation within the short distance class). In contrast, the genetic variation in the Lang Pan Hu (LPH) population (patch LPH-1) was found to be randomly distributed. The different spatial distribution patterns may be attributed to environment differences. These results have implications for the conservation and management of this species, especially for sampling strategies for ex situ conservation.     

On methods of spatial analysis for genotyped individuals

Spatial autocorrelation methods have commonly been applied to individual-based spatial genetic studies, although their properties and the relations among the statistics have not been carefully examined. This paper first introduces a reformulation of widely used spatial statistics using point processes. When Moran's I statistics are applied to allele frequencies within an individual, the frequencies are no longer continuous variables but have only three discrete values and specific interpretations of Moran's I statistics and the number of alleles in common (NAC) can be expressed as the weighted sum of join-count statistics. The distributions of minor genotypes are amplified in Moran's I depending on the allele frequency in the population, while NAC uses a constant weighting system. Under the point process framework, spatial analysis can be conducted on the common theoretical base, from individual locations to genetic distributions of different levels, (for example, genotype and allele). The methodology is demonstrated by application to field data for molecular ecological studies of Fagus crenata population dynamics.     

用分子标记揭示植物随机大居群中亚居群的遗传结构——茅栗自然居群空间遗传结构的SSR分析

采用微卫星标记对茅栗(Castanea sequinii)随机大居群以及其中各亚居群的遗传结构进行了空间自相关分析,以探讨植物自然居群内遗传变异的分布特征及其形成机制。通过9对微卫星引物所产生的119个多态位点,测定了大别山区域内茅栗居群以及各亚居群的空间自相关系数Moran's I值。结果表明:大别山分布的野生茅栗为一个缺乏空间结构的随机大居群,茅栗亚居群之间频繁的花粉流削弱了地理隔离导致的遗传漂变或分化作用在维系居群随机遗传结构中具有的重要作用。但是,在接近亚居群大小的地域范围内(0.228 km)具有一定的空间结构,即小地域尺度中的亚居群存在着空间遗传结构。取样的3个亚居群在小格局范围内都存在一定的空间结构,遗传变异基本上呈非随机分布,在短距离内(61 m)3个亚居群一致表现出不同程度的显著正相关,而随着距离的增加,Moran's I值虽然在不同亚居群间存在一定差异变化,但是总体而言趋向预期值,即不存在空间结构,说明其遗传变异在亚居群内只是在短距离内形成一定的空间结构。研究认为有限的种子散播以及微生境选择等因素可能是产生这种小格局的遗传结构的主要原因。上述研究结果有助于进一步了解植物随机大居群的进化历史和生态过程,同时也为栗属植物中国特有种的保育策略提供了科学依据。     

安徽黄山青冈种群遗传结构的空间自相关分析

以黄山－青冈（Ｃyclobalanopsis glauca)种群为例,研究了种群内等位基因的空间格局,在种群内,大多数等位基因的Moran'sI数大于期望值,但只有两个等位基因存在显著的正空间自相关;如果考虑不同的无性系分株时,大多数等位基因在短距离内存在显著的空间自相关。相关图表明不同距离间隔,Moran'sI指数变化无规律,表明没有哪个进化因子起决定作用,但无性系繁殖在空间自相关中起重要作用,尤其是在近距离。     

Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers

Castanea squinii Dode,an endemic tree widely distributed in China,plays an important role both in chestnut breeding and forest ecosystem function.The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations,and can provide insights into effective conservation of genetic resources.In the present study,the spatial genetic structure of a panmictic natural population of C.sequinii in the Dabie Mountain region was investigated using microsatellite markers.Nine prescreened microsatellite loci generated 29-33 alleles each,and were used for spatial autocorrelation analysis.Based on Moran's I coefficient,a panmictic population of C.sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure.These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C.sequinii populations.Further,a spatial genetic structure was detected in each subpopulation's scale (0.228 km),with all three subpopulations showing significant fine-scale structure.The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran's I positive values).Although Moran's I values varied among the different subpopulations,Moran's I in all the three subpopulations reached the expected values with an increase in distances,suggesting a generally patchy distribution in the subpopulations.The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C.sequinii.These results have important implications for understanding the evolutionary history and ecological process of the natural population of C.sequinii and provide baseline data for formulating a conservation strategy of Castanea species.     

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.     

中国栗疫病菌群体遗传结构的空间自相关性分析

应用空间自相关分析方法对中国栗疫病菌17个居群RAPD遗传变异的空间结构进行研究,以探讨栗疫病菌居群遗传变异的分布特征及其形成机制。结果表明：中国栗疫病菌居群缺乏空间结构,绝大多数RAPD位点变异为随机分布的空间模式,但部分位点表现出渐变、斑块和双向渐变的非随机分布模式,又显示了一定的空间结构。推测其形成原因可能是长距离的基因流、人类活动、地理隔离以及栗疫病菌本身的繁殖特性综合作用的结果,并依据部分位点呈单向渐变的模式推测西南地区为中国栗疫病菌的起源中心。     

Spatial autocorrelation in biology 2. Some biological implications and four applications of evolutionary and ecological interest

Spatial autocorrelation analysis tests whether the observed value of a variable at one locality is significantly dependent on values of the variable at neighbouring localities. The method was extended by us in an earlier paper to include the computation of correlograms for spatial autocorrelation. These show the autocorrelation coefficient as a function of distance between pairs of localities, and summarize the patterns of geographic variation exhibited by the response surface of any given variable. Identical variation patterns lead to identical correlograms, but different patterns may or may not yield different correlograms. Similarity in the correlograms of different variation patterns suggests similarity in the generating mechanism of the pattern.
The inferences that can be drawn from correlograms are discussed and illustrated. Examination and analysis of variation patterns of several characters or gene frequencies for one population, or of several populations in different places or at different times, permit some conclusions about the nature of the populational processes generating the observed patterns.
Autocorrelation analysis is applied to four biological situations differing in the nature of the data (interval or nominal), in the type of grid connecting the localities (regular or irregular), and the field of application (evolution or ecology). The examples comprise genotypes of individual mice, blood group frequencies in humans, gene frequency variation in a perennial herb, and the distribution of species of trees. The implications of our findings are discussed.     

Genetic structure of the human population in the Po delta

The genetic structure of the population of Ferrara Province in the Po delta in Italy was investigated using chi 2 analysis, kinship analysis, analysis of correspondences, and geographical mapping of principal components of gene frequencies. chi 2 Analysis tests for Hardy-Weinberg equilibrium and for heterogeneity of gene and phenotype frequencies; kinship analysis tests for association between indicators of genetic and geographic proximity; analysis of correspondences relates localities and genetic systems in an eigenvectorial space; and geographic mapping displays the principal components of gene frequencies in the real space. In 1,364 adults in 26 residential units, seven presumably neutral isoenzyme systems were typed; ACP1 ESD, GLO I, GPT, PGD, PGM1 and PGP. It was found that average kinship for these neutral systems is correlated with geographic distance in this small area, but not as strongly as kinship for beta-thalassemia. A north-south gradient was observed for ESD. Analysis of correspondences indicated GPT, PGM1, and GLO I as the systems contributing most to differentiation within the province. The maps obtained from principal components of gene frequencies were consistent with the migrational history of the area.     

Migration and genetic structure in Northumberland

To understand the genetic variation that occurs among regions of northern England, we estimated migration from places of birth and residence in the last two generations for a sample of 1367 families in Northumberland. There has been an increase in kinship among regions, compatible with the increased mobility of recent decades, but the kinship patterns suggest that any regional gene frequency differences have remained relatively undiluted. Comparison of kinship and geographic distance between regions indicates that geographic location is an important determinant of genetic structure.     

Spatial genetic structure of two sympatric neotropical palms with contrasting life histories

The spatial genetic structure within sympatric populations of two neotropical dioecious palm species with contrasting life histories was characterized to evaluate the influence of life history traits on the extent of genetic isolation by distance. Chamaedorea tepejilote is a common wind-pollinated arboreal understory palm. Chamaedorea elatior is an uncommon climbing subcanopy palm with entomophilous pollination syndrome. A total of 59 allozyme alleles for C. tepejilote and 53 alleles for C. elatior was analyzed using both unweighted (Iu) and weighted (Iw) Moran's I spatial autocorrelation statistics. The spatial genetic structure detected within these populations is consistent with those reported for highly dispersed plants. A significance test for differences between mean Moran's I-coefficients revealed less spatial genetic structure within the C. tepejilote population than that in the C. elatior population. Adjacent individuals of C. elatior exhibited significant spatial genetic autocorrelation (Iu=0.039, Iw=0.034), indicating a Wright's neighborhood size of about 100 individuals. For C. tepejilote, nonrandom genetic distribution among nearest neighbors was detected, even from small spatial autocorrelation values (Iu=0.008, Iw=0.009), consistent with a neighborhood size of about 300 individuals. For both species, seed dispersal, mortality among life cycle stages, overlapping generations, and contrasting traits of mating and reproduction influence the standing spatial genetic structure within populations.     

Genetic structure of Camellia japonica L. in an old-growth evergreen forest, Tsushima, Japan

The spatial genetic structure of Camellia japonica was investigated, using microsatellite markers, in a 4-ha permanent plot within an old-growth forest. Spatial distribution of individuals was also assessed to obtain an insight into spatial relationships between individuals and alleles. Morisita's index of dispersion showed that 518 C. japonica individuals in the plot were clumped, and Moran's I spatial autocorrelation coefficient revealed weak genetic structure, indicating a low level of allele clustering. Average I correlograms showed that there was stronger genetic structure over short-distance classes. The clumped distribution of individuals and the positive autocorrelation over short-distance classes may result from the limited seed dispersal and microsite heterogeneity of the stand, while the genetic structure may be weakened by overlapping seed shadow and extensive pollen flow, mediated by animal vectors, and the high outcrossing rate found in C. japonica.     

Genetic differentiation among Sardinian villages.

The present study reports an analysis of genetic differentiation among 14 Sardinian villages located mainly in the center of the island. Chi-square tests show significant genetic heterogeneity among villages, and analyses by F- and R- statistics indicate an essentially random pattern of differentiation for all alleles. Using the kinship methods of Morton, a matrix, R, with elements rij describing the correlations between the gene frequencies of villages i and j is obtained. Use of Malécot's formula relating the rij to the geographic distances between villages shows a rapid decline of kinship with increasing distance but reveals essentially no relationship for distances over 40 km. Rotation of a two-dimensional reduction of the kinship matrix to maximum congruence with the geographic distances indicates that about 25% of the genetic distances can be accounted for by the geographic location of the villages. Isolation due in part to cultural factors, genetic drift, and special local or regional patterns of villages associations appear to be involved in the pattern of genetic variation.     

Estimating dispersal from short distance spatial autocorrelation

A series of theoretical studies has formed a strong connection between spatial statistics observed in populations and summary measures of the amount of dispersal. Synthesized, these developments allow dispersal to be indirectly estimated from standing spatial patterns of genetic variation under a range of conditions broad enough to be likely met in most populations of either plants or animals. The spatial correlations at the shortest distances are particularly robust to range of conditions and have disproportionately high statistical power. This review integrates theoretical results in a way that maximizes robustness and flexibility in the use of short distance autocorrelation to estimate Wright's neighborhood size, or the total variance in dispersal distances. Empirical guidelines are developed that are meant to be as practical and broad as possible. The guidelines focus on Moran's I-statistics for diploid genotypes converted to allele frequencies, but are also extended to or compared with several other approaches.     

Spatial autocorrelation in biology 1. Methodology

Spatial autocorrelation analysis tests whether the observed value of a nominal, ordinal, or interval variable at one locality is independent of values of the variable at neighbouring localities. The computation of autocorrelation coefficients for nominal, ordinal, and for interval data is illustrated, together with appropriate significance tests. The method is extended to include the computation of correlograms for spatial autocorrelation. These show the autocorrelation coefficient as a function of distance between pairs of localities being considered, and summarize the patterns of geographic variation exhibited by the response surface of any given variable.
Autocorrelation analysis is applied to microgeographic variation of allozyme frequencies in the snail Helix aspersa. Differences in variational patterns in two city blocks are interpreted.
The inferences that can be drawn from correlograms are discussed and illustrated with the aid of some artificially generated patterns. Computational formulae, expected values and standard errors are furnished in two appendices.     

Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.     

Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods

Three different approaches were used to assess the kinship structure of two epiphytic bryophytes, Orthotrichum speciosum and O. obtusifolium, that have different dispersal strategies. The two species were sampled in a 200 ha landscape where species occurrence and host trees had been mapped previously. Local environmental conditions at sampled trees were recorded and kinship between individuals was calculated based on amplified fragment length polymorphism (AFLP)-marker data. We did not detect any association between AFLP-markers and investigated environmental conditions. In both species, significant kinship coefficients were found between individuals up to 300-350 m apart which shows that both species have a restricted dispersal range. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models (GAMs), but linear regression failed to detect any structure in O. speciosum. Although the dioecious O. obtusifolium is currently the more common species it may, none the less, due to its restricted dispersal range and reproduction mode, become threatened in the future by current silvicultural practices which enhance the distance between host trees and decrease their life span. Finally, GAMs seem most appropriate for analysing spatial genetic structure because the effects of local environmental conditions and spatial structure can be analysed simultaneously, no assumption of a parametric form between kinship coefficient and distance is required, and spatial data resolution is not lost in the arbitrary choice of distance classes characterizing autocorrelation analysis.     

Effects of historical demography and ecological context on spatial patterns of genetic diversity within foxtail pine (Pinus balfouriana; Pinaceae) stands located in the Klamath Mountains, California

The density and dispersion of individuals, nonequilibrium demographics, and habitat fragmentation all affect the magnitude and extent of spatial genetic structure within forest tree populations. Here, we investigate the link between historical demography and spatial genetic structure within ecologically contrasting stands of foxtail pine (Pinus balfouriana) in the Klamath Mountains of northern California. We defined two stand types a priori, based largely on differences in foxtail pine density and basal area, and for each type we sampled two stands. Population expansions, likely from Pleistocene bottlenecks, were detected in three of the four stands. The magnitude and extent of spatial autocorrelation among genotypes at five nuclear microsatellites differed dramatically among stands, with those having lower foxtail pine density exhibiting strong patterns of isolation by distance. Moran's I statistics were 7-fold higher for the first distance class (<25 m) in these stands relative to those observed in stands with higher foxtail pine density (I(25) = 0.14 vs. 0.02). We conclude that differences in spatial genetic structure between stand types are due to differences in ecological attributes that affected expansion from inferred bottlenecks.