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。     

Genetic spatial autocorrelation can readily detect sex-biased dispersal

Sex-biased dispersal is expected to generate differences in the fine-scale genetic structure of males and females. Therefore, spatial analyses of multilocus genotypes may offer a powerful approach for detecting sex-biased dispersal in natural populations. However, the effects of sex-biased dispersal on fine-scale genetic structure have not been explored. We used simulations and multilocus spatial autocorrelation analysis to investigate how sex-biased dispersal influences fine-scale genetic structure. We evaluated three statistical tests for detecting sex-biased dispersal: bootstrap confidence intervals about autocorrelation r values and recently developed heterogeneity tests at the distance class and whole correlogram levels. Even modest sex bias in dispersal resulted in significantly different fine-scale spatial autocorrelation patterns between the sexes. This was particularly evident when dispersal was strongly restricted in the less-dispersing sex (mean distance <200 m), when differences between the sexes were readily detected over short distances. All tests had high power to detect sex-biased dispersal with large sample sizes (n ≥ 250). However, there was variation in type I error rates among the tests, for which we offer specific recommendations. We found congruence between simulation predictions and empirical data from the agile antechinus, a species that exhibits male-biased dispersal, confirming the power of individual-based genetic analysis to provide insights into asymmetries in male and female dispersal. Our key recommendations for using multilocus spatial autocorrelation analyses to test for sex-biased dispersal are: (i) maximize sample size, not locus number; (ii) concentrate sampling within the scale of positive structure; (iii) evaluate several distance class sizes; (iv) use appropriate methods when combining data from multiple populations; (v) compare the appropriate groups of individuals.     

浙江天台山甜槠种群遗传结构的空间自相关分析

采用空间自相关分析方法对浙江天台山亚热带常绿阔叶林优势种甜槠种群全部个体及不同年龄级个体的小尺度空间遗传结构进行了分析,以探讨甜槠种群内遗传变异的分布特征及其形成机制。根据11个ISSR引物所提供的多态位点,经GenAlEx 6软件计算地理坐标和遗传距离矩阵在10个距离等级下的空间自相关系数。在样地内,甜槠种群内个体在空间距离小于10 m时存在显著的正空间遗传结构,其X-轴截矩为9.945。甜槠种群的空间遗传结构与其种子短距离传播和广泛的花粉传播有关。Ⅰ年龄级、Ⅱ年龄级和III年龄级个体在空间距离小于10 m时存在显著的正空间遗传结构,其X-轴截矩分别为11.820、9.746和9.792。当距离等级为5 m时,其空间自相关系数r分别为0.068、0.054和0.070。Ⅳ年龄级个体在所有空间距离等级中均不存在显著的空间遗传结构。甜槠是多年生、长寿命植物,自疏作用是导致IV年龄级个体空间遗传结构消失的主要原因。     

Spatial genetic structure and dispersal of giant pandas on a mountain-range scale

Understanding the spatial genetic structure of populations can provide insight into the ecological or evolutionary processes of the species, and enable wise conservation decisions. We examined the spatial genetic structure of a giant panda (Ailuropoda melanoleuca) population in a heterogeneous mountainous landscape using noninvasive genetic sampling and 12 microsatellite loci. Nonrandom genetic structure was detected through spatial autocorrelation analysis, demonstrating a significantly positive autocorrelation over closer distances. Additional spatial analyses showed significantly positive genetic correlation among spatially-proximate males, and no correlation among females and among male–female pairs. These findings suggest a female-biased dispersal pattern and cryptic family grouping among giant pandas on a large mountain-range scale. The spatial extent of genetic structure occurred within 12.5 km, measured by a least-cost path distance model integrating information of habitat quality and habitat preferences of this species. Using the bearing analysis of PASSAGE, we found that directional genetic autocorrelations were in agreement with habitat structure, and habitat heterogeneity may affect the direction of giant panda dispersal. The characterization of spatial genetic structure can provide potentially valuable information for the conservation and management of giant pandas and their habitat.     

Dispersal, philopatry, and infidelity: dissecting local genetic structure in superb fairy-wrens (Malurus cyaneus)

Dispersal influences evolution, demography, and social characteristics but is generally difficult to study. Here we combine long-term demographic data from an intensively studied population of superb fairy-wrens (Malurus cyaneus) and multivariate spatial autocorrelation analyses of microsatellite genotypes to describe dispersal behavior in this species. The demographic data revealed: (1) sex-biased dispersal: almost all individuals that dispersed into the study area over an eight-year period were female (93%; n = 153); (2) high rates of extragroup infidelity (66% of offspring), which also facilitated local gene dispersal; and (3) skewed lifetime reproductive success in both males and females. These data led to three expectations concerning the patterns of fine-scale genetic structure: (1) little or no spatial genetic autocorrelation among females, (2) positive spatial genetic autocorrelation among males, and (3) a heterogeneous genetic landscape. Global autocorrelation analysis of the genotypes present in the study population confirmed the first two expectations. A novel two-dimensional local autocorrelation analysis confirmed the third and provided new insight into the patterns of genetic structure across the two-dimensional landscape. We highlight the potential of autocorrelation analysis to infer evolutionary processes but also emphasize that genetic patterns in space cannot be fully understood without an appropriate and intensive sampling regime and detailed knowledge of the individuals genotyped.     

Measures of spatial structure in samples of genotypes for multiallelic loci.

Various spatial autocorrelation statistics have been widely used both in theoretical population genetics and to study the spatial distribution of diploid genotypes in many plant and animal populations. However, previous simulation studies have considered only diallelic loci. In this paper, we use a large number of space-time simulations to characterize for the first time the parametric and statistical values of Moran's I-statistics for converted individual genotypes as well as for join-count statistics. A wide range of levels of dispersal and numbers of alleles and allele frequencies are modelled and the results reveal the different general effects of each of these factors on these statistics. We also examine the range of appropriate sampling designs and sizes for which predicted values can be interpolated for specific sampling schemes for any given population genetic field survey. Numbers of alleles and allele frequencies each affect some statistics but not others. The results indicate generally low standard deviations. The results also develop precise and efficient methods of estimating gene dispersal, based on the various autocorrelation measures of standing spatial patterns of genetic variation within populations. The results also extend these methods to loci with multiple alleles, typical of those studied through modern molecular methods.     

Estimation of dispersal distances of the obligately plant‐associated ant Crematogaster decamera

1. In obligate symbioses with horizontal transmission, the population dynamics of the partner organisms are highly interdependent. Host population size limits symbiont number, and distribution of partners is restricted by the presence and thus dispersal abilities of their respective partner. The Crematogaster decamera–Macaranga hypoleuca ant–plant symbiosis is obligate for both partners. Host survival depends on colonisation by its ant partner while foundress queens require hosts for colony establishment. 2. An experimental approach and population genetic analyses were combined to estimate dispersal distances of foundresses in their natural habitat in a Bornean primary rainforest. 3. Colonisation frequency was significantly negatively correlated with distance to potential reproductive colonies. Results were similar for seedlings at natural densities as well as for seedlings brought out in the area experimentally. Population genetic analysis revealed significant population differentiation with an F_ST of 0.041 among foundresses (n = 157) located at maximum 2280 m apart. In genetic spatial autocorrelation, genotypes of foundresses were significantly more similar than expected at random below 550 m and less similar above 620 m. Direct estimation of dispersal distances by pedigree analysis yielded an average dispersal distance of 468 m (maximum 1103 m). 4. For ants that disperse on the wing, genetic differentiation at such small spatial scales is unusual. The specific nesting requirements of the queens and the necessity for queens to find a host quickly could lead to colonisation of the first suitable seedling encountered, promoting short dispersal distances. Nonetheless, dispersal distances of C. decamera queens may vary with habitat or host spatial distribution.     

Microscale variation in alpine grasslands: AFLPs reveal a high level of genotypic diversity in Primula minima (Primulaceae)

The microscale variation and spatial genetic structure of the alpine plant species Primula minima L. was analysed using AFLPs. AFLP analysis based on three primer combinations and 123 fragments revealed no identical genotypes among the 86 studied samples from a 300 × 300 cm plot. Variation within the study plot was high: Nei's gene diversity was 0.22, Shannon's information index 0.33 and the percentage of polymorphic bands was 60.9. Cluster analysis revealed four main groups of genetically similar individuals and mapping these individuals resulted in a clear spatial pattern, with samples from the same group often located close together. The observed microscale structure was corroborated using a Mantel test, which revealed significant correlation of genetic and spatial distances, and by the results of a spatial autocorrelation analysis that indicated a high level of similarity between adjacent samples. An analysis of molecular variance revealed clear differentiation (18%) between the spatial groups. Overall gene flow within the plot was 1.11 and ranged from 0.33 between the spatially most distant groups to 2.33 between directly neighbouring groups. The extraordinary level of diversity detected in this study indicates an unexpectedly strong relevance of reproduction by seed for the species P. minima in alpine grasslands. The strong microscale variation suggests, however, that there is limited dispersal of seeds. Clonal reproduction is of subsidiary importance to sexual reproduction and seems to occur only over very small distances.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 549–556.     

GENE DISPERSAL AND SPATIAL GENETIC STRUCTURE

Spatial autocorrelation statistics have been studied in theoretical population genetic models and widely used in experimental studies of spatial structure in many plant and animal populations. However, the statistical properties of spatial autocorrelation statistics have remained uncharacterized. Little is known about how values of spatial autocorrelation statistics in population samples depend on the level of dispersal and scheme of sampling. In this paper, we characterize the statistical properties of join-count spatial autocorrelation statistics for population genetic surveys under various conditions of dispersal and sampling. The results indicate generally high statistical power. These results can provide a method to estimate gene dispersal based on standing spatial patterns of genetic variation observed within populations.     

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.     

Genetic neighbourhood of clone structures in eelgrass meadows quantified by spatial autocorrelation of microsatellite markers

Limited dispersal distances in plant populations frequently cause local genetic structure, which can be quantified by spatial autocorrelation. In clonal plants, three levels of spatial organization can contribute to positive autocorrelation; namely, the neighbourhood of (a) ramets, (b) clone fragments and (c) entire clones. Here we use data from an exhaustive sampling scheme on a clonal plant to measure the contribution of the neighbourhoods of each distinct clonal structure to total spatial autocorrelation. Four plots (256 grid points each) within dense meadows of the marine clonal plant Zostera marina (eelgrass) were sampled for clone structure with nine microsatellite markers ( approximately 80 alleles). We found significant coancestry (f(ij)), at all three levels of spatial organization, even when not allowing for joins between samples of identical genets. In addition, absolute values of f(ij) and the maximum distance with significant positive f(ij) decreased with the progressive exclusion of joins between alike genotypes. The neighbourhood of this clonal plant thus consists of three levels of organization, which are reflected in different kinship structures. Each of these kinship structures may affect the level of biparental inbreeding and the physical distance between flowering shoots and their outcrossing neighbourhood. These results also emphasize the notion that spatial autocorrelation crucially depends on the scale and intensity of sampling.     

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.     

Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species

Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.     

Pollen and seed flow patterns of Carapa guianensis Aublet. (Meliaceae) in two types of Amazonian forest

Various factors affect spatial genetic structure in plant populations, including adult density and primary and secondary seed dispersal mechanisms. We evaluated pollen and seed dispersal distances and spatial genetic structure of Carapa guianensis Aublet. (Meliaceae) in occasionally inundated and terra firme forest environments that differed in tree densities and secondary seed dispersal agents. We used parentage analysis to obtain contemporary gene flow estimates and assessed the spatial genetic structure of adults and juveniles. Despite the higher density of adults (diameter at breast height ≥ 25 cm) and spatial aggregation in occasionally inundated forest, the average pollen dispersal distance was similar in both types of forest (195 ± 106 m in terra firme and 175 ± 87 m in occasionally inundated plots). Higher seed flow rates (36.7% of juveniles were from outside the plot) and distances (155 ± 84 m) were found in terra firme compared to the occasionally inundated plot (25.4% and 114 ± 69 m). There was a weak spatial genetic structure in juveniles and in terra firme adults. These results indicate that inundation may not have had a significant role in seed dispersal in the occasionally inundated plot, probably because of the higher levels of seedling mortality.     

Pollen dispersal and genetic structure of the tropical tree Dipteryx panamensis in a fragmented Costa Rican landscape

In the face of widespread deforestation, the conservation of rainforest trees relies increasingly on their ability to maintain reproductive processes in fragmented landscapes. Here, we analysed nine microsatellite loci for 218 adults and 325 progeny of the tree Dipteryx panamensis in Costa Rica. Pollen dispersal distances, genetic diversity, genetic structure and spatial autocorrelation were determined for populations in four habitats: continuous forest, forest fragments, pastures adjacent to fragments and isolated pastures. We predicted longer but less frequent pollen movements among increasingly isolated trees. This pattern would lead to lower outcrossing rates for pasture trees, as well as lower genetic diversity and increased structure and spatial autocorrelation among their progeny. Results generally followed these expectations, with the shortest pollen dispersal among continuous forest trees (240 m), moderate distances for fragment (343 m) and adjacent pasture (317 m) populations, and distances of up to 2.3 km in isolated pastures (mean: 557 m). Variance around pollen dispersal estimates also increased with fragmentation, suggesting altered pollination conditions. Outcrossing rates were lower for pasture trees and we found greater spatial autocorrelation and genetic structure among their progeny, as well as a trend towards lower heterozygosity. Paternal reproductive dominance, the pollen contributions from individual fathers, did not vary among habitats, but we did document asymmetric pollen flow between pasture and adjacent fragment populations. We conclude that long-distance pollen dispersal helps maintain gene flow for D. panamensis in this fragmented landscape, but pasture and isolated pasture populations are still at risk of long-term genetic erosion.     

SPATIAL GENETIC STRUCTURE OF CLONAL AND SEXUAL REPRODUCTION IN POPULATIONS OF ADENOPHORA GRANDIFLORA (CAMPANULACEAE)

The spatial distribution of clonal versus sexual reproduction in plant populations should generally have differing effects on the levels of biparental inbreeding and the apparent selfing rate, produced via mating by proximity through limited pollen dispersal. We used allozyme loci, join-count statistics, and Moran's spatial autocorrelation statistics to separate the spatial genetic structure caused by clonal reproduction from that maintained in sexually reproduced individuals in two populations of Adenophora grandiflora, a perennial herb. Join-count statistics showed that there were statistically significant clustering of clonal genotypes within distances less than 4 m. Both the entire populations and the sets of sexually reproduced individuals exhibited significant spatial autocorrelation at less than about 12 m, and the sexually reproduced individuals are substantially structured in an isolation-by-distance manner, consistent with a neighborhood size of about 50.     

Genetic structure of age classes in Camellia japonica (Theaceae)

Camellia japonica L. (Theaceae), an insect- and bird-pollinated, broad-leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L-shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F-statistics, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m x 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's I-statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisita's index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self-thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self-thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.     

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.     

Understanding age-specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis

Many marine species have vastly different capacities for dispersal during larval, juvenile and adult life stages, and this has the potential to complicate the identification of population boundaries and the implementation of effective management strategies such as marine protected areas. Genetic studies of population structure and dispersal rarely disentangle these differences and usually provide only lifetime-averaged information that can be considered by managers. We address this limitation by combining age-specific autocorrelation analysis of microsatellite genotypes, hydrodynamic modelling and genetic simulations to reveal changes in the extent of dispersal during the lifetime of a marine fish. We focus on an exploited coral reef species, Lethrinus nebulosus, which has a circum-tropical distribution and is a key component of a multispecies fishery in northwestern Australia. Conventional population genetic analyses revealed extensive gene flow in this species over vast distances (up to 1,500 km). Yet, when realistic adult dispersal behaviours were modelled, they could not account for these observations, implying adult dispersal does not dominate gene flow. Instead, hydrodynamic modelling showed that larval L. nebulosus are likely to be transported hundreds of kilometres, easily accounting for the observed gene flow. Despite the vast scale of larval transport, juvenile L. nebulosus exhibited fine-scale genetic autocorrelation, which declined with age. This implies both larval cohesion and extremely limited juvenile dispersal prior to maturity. The multidisciplinary approach adopted in this study provides a uniquely comprehensive insight into spatial processes in this marine fish.     

Spatial genetic structure in populations of the terrestrial orchid Orchis cyclochila (Orchidaceae)

Orchid seeds are minute, dust-like, wind-borne and, thus, would seem to have the potential for long-distance dispersal. Based on this perception, one may predict near-random spatial genetic structure within orchid populations. In reality we do not know much about seed dispersal in orchids and the few empirical studies of fine-scale genetic structure have revealed significant genetic structure at short distances (< 5m), suggesting that most seeds of orchids fall close to the maternal plant. To obtain more empirical data on dispersal, Ripley’s L(d)-statistics, spatial autocorrelation analyses (coancestry, f_ij analyses) and Wright’s F statistics were used to examine the distribution of individuals and the genetic structure within two populations of the terrestrial orchid Orchis cyclochila in southern Korea. High levels of genetic diversity (H_e = 0.210) and low between-population variation were found (F_ST = 0.030). Ripley’s L(d)-statistics indicated significant aggregation of individuals, and patterns varied depending on populations. Spatial autocorrelation analysis revealed significant positive genetic correlations among individuals located <1 m, with mean f_ij values expected for half sibs. This genetic structure suggests that many seeds fall in the immediate vicinity of the maternal plant. The finding of significant fine-scale genetic structure, however, does not have to preclude the potential for the long distance dispersal of seeds. Both the existence of fine-scale genetic structure and low F_ST are consistent with a leptokurtic distribution of seed dispersal distances with a very flat tail.