Spatial Structure Of Genetic Variation Research Articles

Fine-scale spatial genetic structure, neighbourhood size and gene dispersal in clonal plants: exploring the best possible estimates

AbstractGene movement in plants is determined by seed and pollen flow and its limitation results in spatial structuring of genetic variation, affecting potential levels of inbreeding within populations. In clonal plants, clonal propagation may also play an important role in spatial genetic structure (SGS). Characterization of SGS usually is done by analysing several spatial scales with large sample sizes to ensure a reliable measure. Several sampling strategies are available, but most are not suitable for clonal plants. Here, two sampling strategies were used to characterize within-population SGS structure and gene dispersal in a natural population of the clonal species Aechmea nudicaulis (Bromeliaceae) and the results between them were compared. The first was based on exhaustive sampling in a rectangular closed area, and the second was a stratified design along a linear transect. Different intensities and patterns of SGS were detected for each design and the linear design revealed stronger SGS over a wider range. The significant SGS revealed a restricted dispersal and comparisons of sexual versus vegetative components of gene dispersal suggest that clonal spread can be at least as important as sexual reproduction. Thus, the results suggest that for clonal plants the best strategy is the combination of both sampling schemes since each one unveils important aspects of spatial structure of the population.

Évolution et adaptation fonctionnelle des arbres tropicaux : le cas du genre <I>Guibourtia</I> Benn.

La présente thèse s’intéresse aux mécanismes à l’origine de la diversification des espèces d’arbres tropicaux. Elle utilise le genre Guibourtia Benn. (Fabaceae-Detarioideae) comme modèle biologique afin de comprendre les mécanismes historiques, biologiques et environnementaux à l’origine de la diversité de ce genre. Plus particulièrement, elle vise, d’une part, à étudier, au niveau interspécifique, le rôle relatif des forces évolutives neutres et de sélection dans la diversification du genre Guibourtia et, d’autre part, au niveau intra-spécifique, à questionner les causes de la différenciation des populations de trois espèces de Guibourtia. Au niveau interspécifique, la phylogénie datée basée sur le séquençage du génome chloroplastique complet a globalement confirmé la taxonomie actuelle. Elle a montré une diversification au milieu du Miocène en trois clades qui sont décrits aujourd’hui comme des sous-genres (Guibourtia, Gorskia et Pseudocopaiva). Elle démontre en outre que deux espèces américaines sont issues d’une migration de l’Afrique vers l’Amérique à la fin du Miocène. Il est également apparu que certains traits morphologiques ont été sélectionnés de manière convergente au sein des différents clades du genre Guibourtia en fonction des niches climatiques des espèces. Ce dernier résultat a été consolidé au moyen d’une expérimentation écophysiologique prouvant que la lumière constitue un important facteur de sélection et de différenciation adaptative entre certaines espèces du genre. Au niveau intraspécifique, une étude de phylogéographie a permis de mettre en évidence que les barrières biogéographiques chez G. ehie et les gradients climatiques chez G. coleosperma auraient contribué à la différenciation génétique des populations. En outre, cette étude montre une forte différenciation entre les populations de G. ehie d’Afrique de l’Ouest et d’Afrique centrale, en lien avec quelques traits morphologiques, ce qui préjuge de l’existence d’une nouvelle espèce. Enfin, chez G. tessmannii, espèce aux fruits déhiscents et graines arillées, nous avons identifié les principaux disperseurs dont les calaos (Ceratogymna atrata) qui pourraient contribuer à une dispersion à longue distance, influençant la structure spatiale de la variation génétique des populations. Cette thèse, en utilisant le genre Guibourtia comme modèle d’étude, a apporté de nouveaux éléments à la compréhension des mécanismes qui génèrent la diversité au sein des espèces d’arbres.

Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor).

Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring.

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.

Habitat saturation and the spatial evolutionary ecology of altruism

Under which ecological conditions should individuals help their neighbours? We investigate the effect of habitat saturation on the evolution of helping behaviours in a spatially structured population. We combine the formalisms of population genetics and spatial moment equations to tease out the effects of various physiological (direct benefits and costs of helping) and ecological parameters (such as the density of empty sites) on the selection gradient on helping. Our analysis highlights the crucial importance of demography for the evolution of helping behaviours. It shows that habitat saturation can have contrasting effects, depending on the form of competition (direct vs. indirect competition) and on the conditionality of helping. In our attempt to bridge the gap between spatial ecology and population genetics, we derive an expression for relatedness that takes into account both habitat saturation and the spatial structure of genetic variation. This analysis helps clarify discrepancies in the results obtained by previous theoretical studies. It also provides a theoretical framework taking into account the interplay between demography and kin selection, in which new biological questions can be explored.

Spatial genetic and clonal structure inMaianthemum dilatatumas defined by AFLP markers

Amplified fragment length polymorphisms (AFLPs) were used to investigate the clonal and spatial genetic structure of Maianthemum dilatatum (A. Wood) Nels. & J.F. Macbr. (Convallariaceae), a clonal rhizomatous herb, which can form large patches of continuous cover. Within a subpopulation covering approximately 3 ha, all patches (n = 21) were mapped and sampled. Within these patches, 116 ramets were sampled and assigned to 74 putative genets. Small patches appeared to be single genets while larger patches were genetically heterogeneous and only moderately differentiated (ΦST= 0.291, p = 0.001). Less intense sampling in other populations produced similar results in that single genet populations were not found. Evidence of genet natality was present with the detection of five yearlings within a single season. Spatial autocorrelation measures detected spatial genetic structure attributable to both clonal growth and gene flow processes. It was concluded that within M. dilatatum populations, clonality is a significant factor, but the spatial structuring of genetic variation suggests that both low levels of restricted gene flow and repeated recruitment of genets occur.

Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion

In habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono-sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early- and late-succession populations in a landscape where extinction and recolonization are recurrent (the 'Grand Brûlé') and for late-succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; F(ST) values among early- and among late-succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, F(IS) values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late-succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high F(IS) values.

Mutation at high rates reduces spatial structure within populations

The question of whether or not the high rates (mu) of mutation that occur for some hypervariable markers can affect commonly used empirical measures of spatial structure of genetic variation within populations is addressed. The results show that values of these measures are approximately halved when mu is 10(-2). Finest spatial-scale correlations, measured by either Moran's I-statistics or conditional kinship, are reduced by 30%-50%. When the mutation rate is 10 times lower, much smaller reductions result, e.g. averaging 7% for the finest scale correlations. Still smaller orders of magnitude of mu cause negligible changes in spatial structure, where any effects normally would not be detectable. The reductions are caused by forward mutations, and when the reductions are measured as percentages, they are nearly independent of the amount of structure produced sans mutation, except when dispersal is nearly minimal. The percent reductions are also nearly independent of the number of alleles and of back mutations, hence of the nature of the mutation process (e.g. stepwise or not). The results demonstrate that some hypervariable loci should have reduced spatial structuring, and that marker choice may affect the values observed in experimental surveys. Moreover, if fine-scale correlations are used to indirectly estimate dispersal distances, then mutation at high rates could inflate estimates, easily up to two- to three-fold.

Microsatellite analysis of spatial structure among seedlings in populations of Pinus strobus (pinaceae)

In a detailed analysis of how limited seed dispersal can create spatial structuring of genetic variation, several nuclear microsatellites were assayed in seedlings from two forests of Pinus strobus, one old growth (OG) and the other (second site, SS) logged in ca. 1900. By using loci with a large number of alleles and new statistical methods on averaged spatial correlation coefficients, unusually precise estimates of spatial genetic structure were obtained, even though the structure was expected to be very weak. This high precision allowed the spatial patterns to be contrasted across loci and populations. At the OG site, the average spatial correlation coefficient for short distances (<15 m) exceeded its random expected value by 0.035, providing an indirect estimate of ca. 230 for Wright's neighborhood size. The value is similar to that estimated in a previous study of adult trees at OG and probably represents the natural level of spatial structure. A very similar value, 0.030, was obtained for seedlings at SS, despite the fact that unlike OG, genotypes of adults are randomly distributed, a likely result of logging. The results show that a single cycle of limited seed dispersal recreated the natural level of spatial structuring. In addition, one microsatellite, Rps50, had far greater amounts of allele variation, likely implicating it as having a higher mutation rate. The spatial structure of Rps50 also was significantly reduced, in a way that could be consistent with theoretical effects of high mutation rates (up to μ = 10(-2)). The choice of markers may influence estimates of spatial genetic structure. For example, if Rps50 is omitted the values are nearly doubled to 0.058 and 0.051 for SS and OG, respectively, both indicating a much smaller neighborhood size of ca. 100.

Multilocus estimation of genetic structure within populations

Spatial structure of genetic variation within populations is well measured by statistics based on the distribution of pairs of individual genotypes, and various such statistics have been widely used in experimental studies. However, the problem of uncharacterized correlations among statistics for different alleles has limited the applications of multiallelic, multilocus summary measures, since these had unknown sampling distributions. Usually multiple alleles and/or multiple loci are required in order to precisely measure spatial structures, and to provide precise indirect estimates of the amount of dispersal in samples of reasonable size. This article examines the correlations among pair-wise statistics, including Moran I-statistics and various measures of conditional kinship, for different alleles of a locus. First the correlations are mathematically derived for random spatial distributions, which allow averages over alleles and loci to be used as more powerful yet exact test statistics for the null hypothesis. Then extensive computer simulations are conducted to examine the correlations among values for different alleles under isolation by distance processes. For loci with more than three alleles, the results show that the correlations are remarkably and perhaps surprisingly small, establishing the principle that then alleles behave as nearly independent realizations of space–time stochastic processes. The results also show that the correlations are largely robust with respect to the degree of spatial structure, and they can be used in a straightforward manner to form confidence intervals for averages. The results allow a precise connection between observations in experimental studies and levels of dispersal in theoretical models.

Spatial structure of AFLP genetic diversity of remnant populations of Metasequoia glyptostroboides (Taxodiaceae)

The Tertiary relic species, Metasequoia glyptostroboides, is naturally distributed in a narrowly restricted area bordering Hubei, Hunan Provinces and Chongqing City in central China. The genetic background of its overall genetic diversity and population structure is prerequisite for formulating an efficient conservation program and effective practice in management of remnant populations. The spatial structure of gene frequencies of M. glyptostroboides remnant populations in its original habitat was investigated using AFLP markers followed by spatial autocorrelation analysis. A total of 39 individuals were sampled from remnant populations and subjected to spatial autocorrelation analysis in two approaches of equal gene frequency correlograms with five classes and equal distance interval correlograms with ten classes, respectively. Of 46 polymorphic bands generated by six selective primer-pairs, 27 polymorphic bands with frequencies ranging from 25% to 75% were then used to calculate Moran's I spatial autocorrelation coefficient. The result revealed a lack of spatial structure of genetic variation existing in the remnant population of M. glyptostroboides, indicating that genetic variations of the most polymorphic loci were randomly distributed, strongly supported by insignificant Moran's I coefficients. However, lump, depression or double cline structures of the genetic variation were found in a few AFLP markers with significant Moran's I in several distance classes. The distance interval 4-8 km is probably a sufficient barrier to gene flow, as evidenced by Moran's I coefficients showing negative correlations within this distance class. In addition, remnant individuals were not absent in distance classes from 12 to 28 km, suggesting that the habitat of the remnant populations had been disturbed since humans moved in and subsequent agricultural activities occurred. Apparently, habitat fragmentation resulted in an island distribution and genetic drift had occurred even before M. glyptostroboides was rediscovered in 1941. Based on the results of the present study combined with the lower genetic diversity previously detected in the remnant populations, possible mechanisms causing the endangerment of M. glyptostroboides are discussed and a conservation strategy for M. glyptostroboides remnant populations is proposed. The results provide valuable information for formulating future in situ and ex situ conservation programs of this relic species.

Comparison of fine-scale genetic structure using nuclear microsatellites within two British oakwoods differing in population history

Two oak woods in northern Britain which contained both Quercus robur and Quercus petraea were selected for study. The woods differed in the degree of human interference they had experienced; Roudsea, in the Lake District, is a native wood with no record of planting but has experienced coppicing; Dalkeith, in southern Scotland, has experienced extensive planting and management. All the trees in a selected area of each wood (nearly 700 trees) were mapped and genotyped using six nuclear microsatellite loci. A range of statistical methods was used to assess the diversity and degree of spatial genetic structure present in each wood, and results are compared with published results for a natural oakwood in central France (Petite Charnie). For the unplanted wood at Roudsea, significantly higher genetic diversity and greater spatial genetic structure, at relatively short distances, was detected in the Q. petraea component of the wood relative to that of Q. robur. These observations agree with those from Petit Charnie and indicate that native oak woods across Europe maintain similar levels and structure of genetic variation, and is probably due to differences in seed dispersal mechanism and regeneration dynamics of the species. At Dalkeith, however, significant spatial structure of genetic variation occurred in both species examined, and the additional influence of planting is offered to account for increased genetic structure within this wood. At Roudsea, the influence of coppicing is also discussed to explain the lack of population genetic equilibrium and increased genetic diversity at this site.

Spatial autocorrelation study of population genetic structure of two orchid species

The spatial pattern or structure of genetic variation within populations is an important part of evolutionary and ecological genetic processes in natural populations of plants, and may provide deep insight into the conservation of endangered species. In this paper, we investigated the spatial distribution patterns of population genetic variation of two orchid species, Paphiopedilum micranthum and Changnienia amoena , using RAPD markers. A total of 89 and 42 individuals in two populations of each of the species, respectively, were involved in our study. Based on the polymorphic bands generated by 12 ( P. micranthum ) and 16 ( C. amoena ) RAPD primers, Moran′s I spatial autocorrelation coefficient was calculated, which revealed significant spatial structure of genetic variation within populations of P. micranthum (with significant positive autocorrelation over short distance class: 3～4 m). In contrast, the genetic variation in C. amoena populations was found to be randomly distributed. The different spatial distribution patterns may be attributed to the different reproductive systems of these two species. P. micranthum undergoes significant clonal growth while no significant clonal reproduction was found in C. amoena . These results have important implications for the conservation and management of these species, especially for the sampling strategies for ex situ conservation.

LIMITED SEED DISPERSAL AND GENETIC STRUCTURE IN LIFE STAGES OF CECROPIA OBTUSIFOLIA.

Many pioneer tropical trees have high outcrossing rates. Inbreeding occurs primarily by matings between neighboring relatives. Consequently the manner in which inbreeding levels and heterozygosity change through decreases in effective population size, which may arise, for example, from habitat fragmentation, depends primarily on the degree of spatial structure. Spatial structure could also influence populations' adaptive responsiveness to microenvironmental selection (Epperson 1992). Yet it has been underappreciated that genetic structure should also depend on the life history and life stage of individuals. This paper investigates the importance of seed dispersal on the population genetics and structure of Cecropia obtusifolia, a Neotropical pioneer rainforest tree that is outcrossing and wind pollinated, with seeds that are dispersed by various frugivores. The results show that the type of dispersal system of C. obtusifolia causes marked genetic spatial autocorrelations among the often large numbers of seedlings concentrated within canopy gaps. However, this structure persists in a much weaker relict form in juveniles and adults, probably because by then competition has removed most individuals. The structure of genetic variation has a number of implications for ecological and evolutionary genetics and conservation biology. The level of spatial structure both influences and is influenced by most population genetic factors (Wright 1978). In plant populations, it is intimately connected to levels of pollen and seed dispersal; and studies of spatial structure can be used to estimate dispersal levels (e.g., Epperson 1993). Levels of inbreeding, inbreeding depression, and population survival all can depend on the form and magnitudes of spatial structure of genetic variation (e.g., Wright 1978). It has often been predicted that plant populations with limited seed dispersal should exhibit marked spatial structure even if pollen disperses long distances (e.g., Libby et al. 1969). Yet, in many cases structure has not been detected using Fstatistics. More specifically, genetic correlations among progeny, clustered near their maternal parent because of limited seed dispersal, are predicted to result in substantial genetic structure. However, striking changes in structure can occur as the progeny age, because of a number of often uncited life-history considerations. Primary among these is that many of the correlations among progeny are due to the progeny occuring in much higher densities than the parents. The correlations may greatly diminish as the progeny mature and are thinned out (Epperson 1992). For example, in species (like C. obtusifolia) where seedling recruitment occurs primarily from a single or few age classes and only a small proportion of seedlings survive to replace adults, this kind of structure would essentially disappear. In such cases, and where either pollen or seed disperses relatively long distances, there should be little build up of isolation by distance, even in large continuous populations (Wright 1946). Structure has been found among young progeny of remaining trees (with wind-dispersed pollen) following harvest removal of (long-lived) temperate forest tree species (Neale and Adams 1985; Yazdoni et al. 1985; Furnier et al. 1987), and similar progeny clustering was found in progeny groups of tropical tree species (Sakai 1985). In contrast, little evidence of structure is found among mature adults (Epperson and Allard 1989; Knowles 1990; Schnabel and Hamrick 1990; Perry and Knowles 1991). These results have been sometimes viewed as discrepant (e.g., Schnabel and Hamrick 1990; Perry and Knowles 1991). As noted above, such apparent discrepancies can be explained simply by progeny thinning. However, the forms of structure for two or more life stages are rarely analyzed in the same populations or even in the same species (for an exception see Linhart et al. 1981). It should be noted that strong spatial structure is detected in adult individuals in plant populations with low pollen and seed dispersal (e.g., Schaal 1975; Epperson and Clegg 1986; Schoen and Latta 1989). Cecropia obtusifolia is a Neotropic pioneer tree species that is an important component of subtropical forest canopy. It regenerates strictly in recent gaps in the rainforest canopy. One population of C. obtusifolia has been extensively mapped and studied for allozyme variation, including large amounts of mapped genotypic data for a number of life-cycle stages, including adults, juveniles, and seedlings. Population data from multiple life stages of C. obtusifolia (Alvarez-Buylla et al. 1996) afford an exceptional opportunity to measure and examine the degree of progeny clustering resulting from correlated seed dispersal, and details of the dispersal and structure-forming processes. In this paper we also test the limits to structure detectability, by utilizing very sensitive spatial autocorrelation measures known as join-count statistics (e.g., Epperson 1993) for such structures at various life stages.

Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics.

Spatial structure of genetic variation within populations, an important interacting influence on evolutionary and ecological processes, can be analyzed in detail by using spatial autocorrelation statistics. This paper characterizes the statistical properties of spatial autocorrelation statistics in this context and develops estimators of gene dispersal based on data on standing patterns of genetic variation. Large numbers of Monte Carlo simulations and a wide variety of sampling strategies are utilized. The results show that spatial autocorrelation statistics are highly predictable and informative. Thus, strong hypothesis tests for neutral theory can be formulated. Most strikingly, robust estimators of gene dispersal can be obtained with practical sample sizes. Details about optimal sampling strategies are also described.

Associations between Allele Frequencies in Festuca Ovina and Habitat Variation in the Alvar Grasslands on the Baltic Island of Oland

1 If different genotypes have different relative fitnesses in different habitats, genetic diversity may be maintained in local populations by habitat selection. The spatial structuring of genetic variation within plant populations will thus be associated

Spatial structure of genetic variation within populations of forest trees

The spatial pattern and structure of genetic variation are important aspects of the population genetics of forest stands. Combined with limits to seed and pollen dispersal, spatial structure affects the level of inbreeding and the action of natural selection. The genetic constitution of stand regeneration, following different forestry practices, is also influenced by spatial structure. For example, natural regeneration with seed trees involves sampling seed trees from a stand that may be genetically nonhomogeneous. This paper reviews theoretical and empirical results on spatial patterns of genetic variation, produced under limited gene flow and selection, in terms of recently developed spatial statistics (e.g., spatial autocorrelation). Genetic correlations in samples from spatially structured populations are also described, as well as how spatial samples can be used to characterize the structure of genetic variation, and how inferences can be made about (spatially distributed) components of fitness and yield.

MICROGEOGRAPHIC GENETIC STRUCTURE OF MORPHOLOGICAL AND LIFE HISTORY TRAITS IN A NATURAL POPULATION OF IMPATIENS CAPENSIS.

To investigate the microgeographic spatial structure of genetic variation for quantitative traits in a natural population of Impatiens capensis, we performed a common-garden greenhouse experiment. Seedlings were collected at 10-m intervals from a 40 times 40-m permanent grid in a natural population and grown to maturity in a greenhouse. From these parents, 3 self-fertilized seed families per grid point were then grown in a randomized design in the greenhouse and scored for a variety of morphological and life-history traits. Virtually all of the traits displayed significant variation among families, and many were significantly heterogeneous among grid points, indicating microgeographic genetic differentiation on a fine spatial scale. Overall morphological divergence, measured as Mahalanobis distances between grid points, increased with geographical distance. In general, spatial autocorrelation coefficients of grid point character means were positive at 11-20 m and negative beyond 40 m, although power for significance testing was low. The first factor in a principal component analysis of grid point means was positively loaded on height-related traits and negatively loaded on total reproduction at 50 days, accounting for 31% of the variation. This factor displayed significant positive spatial autocorrelation at 11-20 m and negative autocorrelation at >40 m. The remaining factors showed no detectable spatial structuring among grid points. These differences in spatial pattern among characters suggest that forces other than drift may have influenced the genetic structure of the population. There was no evidence for density-dependent selection; seedling density was not significantly correlated with the grid point mean of any trait.