Plant dispersal, neighbourhood size and isolation by distance

Genetic Structure of Natural Northern Range-Margin Mainland, Peninsular, and Island Populations of Northern Red Oak (Quercus rubra L.)

Plant populations at the leading edge of the species’ native range often exhibit genetic structure as a result of genetic drift and adaptation to harsh environmental conditions. Hence, they are likely to harbour rare genetic adaptations to local environmental conditions and therefore are of particular interest to understand climate adaptation. We examined genetic structure of nine northern marginal mainland, peninsular and isolated island natural populations of northern red oak (Quercus rubraL.), a valuable long-lived North American hardwood tree species, covering a wide climatic range, using 17 nuclear microsatellites. We found pronounced genetic differentiation of a disjunct isolated island population from all mainland and peninsular populations. Furthermore, we observed remarkably strong fine-scale spatial genetic structure (SGS) in all investigated populations. Such high SGS values are uncommon and were previously solely observed in extreme range-edge marginal oak populations in one other study. We found a significant correlation between major climate parameters and SGS formation in northern range-edge red oak populations, with more pronounced SGS in colder and drier regions. Most likely, the harsh environment in leading edge populations influences the density of reproducing trees within the populations and therefore leads to restricted overlapping of seed shadows when compared to more central populations. Accordingly, SGS was negatively correlated with effective population size and increased with latitude of the population locations. The significant positive association between genetic distances and precipitation differences between populations may be indicative of isolation by adaptation in the observed range-edge populations. However, this association was not confirmed by a multiple regression analysis including geographic distances and precipitation distances, simultaneously. Our study provides new insights in the genetic structure of long-lived tree species at their leading distribution edge.

Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei

PREMISE

The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures.

METHODS

To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences.

RESULTS

We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation.

CONCLUSIONS

Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.

Isolation by phenology synergizes isolation by distance across a continuous landscape

Pollen is generally dispersed over short distances, which promotes population genetic structure across continuous two-dimensional space. Quantitative genetic variance in flowering time structures mating pools in the temporal dimension, at least with respect to the phenology loci. We asked if these two phenomena, isolation by distance (IBD) and isolation by phenology (IBP), synergistically promote genetic structure. We constructed an individual-based model that tracked genotype frequencies at flowering time and neutral loci across a uniform landscape, over multiple generations, under four mating schemes: panmixia, IBD only, IBP only, and IBP × IBD. IBD × IBP divided the population into spatial clusters of early-, mid-, and late-flowering genotypes and strongly increased its quantitative genetic variance. Flowering time did not cluster under IBP, but its genetic variance increased moderately. IBD induced mild spatial structure in a nonassortative reference trait but did not change its variance. Importantly, the spatial correlation of genotypes at neutral loci was twice as strong under IBD × IBP compared with IBD alone. IBD × IBP also drew neutral loci into gametic disequilibrium with flowering time loci, structuring them temporally. Temporal and spatial mating pool structure promotes local differentiation. This trend would facilitate adaptation on small spatial scales.

Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, interpopulation genetic differentiation was 6-9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4-7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

The effect of the dispersal kernel on isolation-by-distance in a continuous population

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of neighborhood size as a measure of an effective, local panmictic population is valid for popular families of dispersal distributions. We further show how to draw random variables from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important.

Dioecy, more than monoecy, affects plant spatial genetic structure: the case study of Ficus

In this analysis, we attempt to understand how monoecy and dioecy drive spatial genetic structure (SGS) in plant populations. For this purpose, plants of the genus Ficus were used as a comparative model due to their particular characteristics, including high species diversity, variation in life histories, and sexual systems. One of the main issues we assessed is whether dioecious fig tree populations are more spatially genetically structured than monoecious populations. Using the Sp statistic, which allows for quantitative comparisons among different studies, we compared the extent of SGS between monoecious and dioecious Ficus species. To broaden our conclusions we used published data on an additional 27 monoecious and dioecious plant species. Furthermore, genetic diversity analyses were performed for two monoecious Ficus species using 12 microsatellite markers in order to strengthen our conclusions about SGS. Our results show that dioecy, more than monoecy, significantly contributes to SGS in plant populations. On average, the estimate of Sp was six times higher for dioecious Ficus species than monoecious Ficus species and it was two times higher in dioecious than monoecious plant species. Considering these results, we emphasize that the long-distance pollen dispersal mechanism in monoecious Ficus species seems to be the dominant factor in determining weak spatial genetic structure, high levels of genetic diversity, and lack of inbreeding. Although Ficus constitute a model species to study SGS, a more general comparison encompassing a wider range of plants is required in order to better understand how sexual systems affect genetic structure.

Higher fine-scale genetic structure in peripheral than in core populations of a long-lived and mixed-mating conifer--eastern white cedar (Thuja occidentalis L.)

Background

Fine-scale or spatial genetic structure (SGS) is one of the key genetic characteristics of plant populations. Several evolutionary and ecological processes and population characteristics influence the level of SGS within plant populations. Higher fine-scale genetic structure may be expected in peripheral than core populations of long-lived forest trees, owing to the differences in the magnitude of operating evolutionary and ecological forces such as gene flow, genetic drift, effective population size and founder effects. We addressed this question using eastern white cedar (Thuja occidentalis) as a model species for declining to endangered long-lived tree species with mixed-mating system.

Results

We determined the SGS in two core and two peripheral populations of eastern white cedar from its Maritime Canadian eastern range using six nuclear microsatellite DNA markers. Significant SGS ranging from 15 m to 75 m distance classes was observed in the four studied populations. An analysis of combined four populations revealed significant positive SGS up to the 45 m distance class. The mean positive significant SGS observed in the peripheral populations was up to six times (up to 90 m) of that observed in the core populations (15 m). Spatial autocorrelation coefficients and correlograms of single and sub-sets of populations were statistically significant. The extent of within-population SGS was significantly negatively correlated with all genetic diversity parameters. Significant heterogeneity of within-population SGS was observed for 0-15 m and 61-90 m between core and peripheral populations. Average Sp, and gene flow distances were higher in peripheral (Sp = 0.023, σ_g = 135 m) than in core (Sp = 0.014, σ_g = 109 m) populations. However, the mean neighborhood size was higher in the core (Nb = 82) than in the peripheral (Nb = 48) populations.

Conclusion

Eastern white cedar populations have significant fine-scale genetic structure at short distances. Peripheral populations have several-folds higher within-population fine-scale genetic structure than core populations. Anthropogenic disturbances and population fragmentation presumably have significant effects on fine-scale genetic structure in eastern white cedar. Core populations have higher neighborhood size than peripheral populations, whereas gene flow distances are higher in peripheral than in core populations. The results of our study contribute to the knowledge of poorly-understood spatial genetic structure of core versus peripheral populations in plants. As well, the information is of significance for conservation of genetic resources of eastern white cedar and perhaps of other long-lived forest trees with mixed-mating system.

Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure

Climatic conditions and landscape features often strongly affect species' local distribution patterns, dispersal, reproduction and survival and may therefore have considerable impacts on species' fine-scale spatial genetic structure (SGS). In this study, we demonstrate the efficacy of combining fine-scale SGS analyses with isotropic and anisotropic spatial autocorrelation techniques to infer the impact of wind patterns on plant dispersal processes. We genotyped 1304 Azorella selago (Apiaceae) specimens, a wind-pollinated and wind-dispersed plant, from four populations distributed across sub-Antarctic Marion Island. SGS was variable with Sp values ranging from 0.001 to 0.014, suggesting notable variability in dispersal distance and wind velocities between sites. Nonetheless, the data supported previous hypotheses of a strong NW-SE gradient in wind strength across the island. Anisotropic autocorrelation analyses further suggested that dispersal is strongly directional, but varying between sites depending on the local prevailing winds. Despite the high frequency of gale-force winds on Marion Island, gene dispersal distance estimates (σ) were surprisingly low (<10 m), most probably because of a low pollen dispersal efficiency. An SGS approach in association with isotropic and anisotropic analyses provides a powerful means to assess the relative influence of abiotic factors on dispersal and allow inferences that would not be possible without this combined approach.

Quantifying the lag time to detect barriers in landscape genetics

Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individual-based simulations to examine the ability of an individual-based statistic [Mantel's r using the proportion of shared alleles' statistic (Dps)] and population-based statistic (FST ) to detect barriers. We simulated a range of movement strategies including nearest neighbour dispersal, long-distance dispersal and panmixia. The lag time for the signal of a new barrier to become established is short using Mantel's r (1-15 generations). FST required approximately 200 generations to reach 50% of its equilibrium maximum, although G'ST performed much like Mantel's r. In strong contrast, FST and Mantel's r perform similarly following the removal of a barrier formerly dividing a population. Also, given neighbour mating and very short-distance dispersal strategies, historical discontinuities from more than 100 generations ago might still be detectable with either method. This suggests that historical events and landscapes could have long-term effects that confound inferences about the impacts of current landscape features on gene flow for species with very little long-distance dispersal. Nonetheless, populations of organisms with relatively large dispersal distances will lose the signal of a former barrier within less than 15 generations, suggesting that individual-based landscape genetic approaches can improve our ability to measure effects of existing landscape features on genetic structure and connectivity.

Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis

Measures of genetic structure among individuals or populations collected at different spatial locations across a landscape are commonly used as surrogate measures of functional (i.e. demographic or genetic) connectivity. In order to understand how landscape characteristics influence functional connectivity, resistance surfaces are typically created in a raster GIS environment. These resistance surfaces represent hypothesized relationships between landscape features and gene flow, and are based on underlying biological functions such as relative abundance or movement probabilities in different land cover types. The biggest challenge for calculating resistance surfaces is assignment of resistance values to different landscape features. Here, we first identify study objectives that are consistent with the use of resistance surfaces and critically review the various approaches that have been used to parameterize resistance surfaces and select optimal models in landscape genetics. We then discuss the biological assumptions and considerations that influence analyses using resistance surfaces, such as the relationship between gene flow and dispersal, how habitat suitability may influence animal movement, and how resistance surfaces can be translated into estimates of functional landscape connectivity. Finally, we outline novel approaches for creating optimal resistance surfaces using either simulation or computational methods, as well as alternatives to resistance surfaces (e.g. network and buffered paths). These approaches have the potential to improve landscape genetic analyses, but they also create new challenges. We conclude that no single way of using resistance surfaces is appropriate for every situation. We suggest that researchers carefully consider objectives, important biological assumptions and available parameterization and validation techniques when planning landscape genetic studies.

Investigating the effects of topography and clonality on genetic structuring within a large Norwegian population of Arabidopsis lyrata

BACKGROUND AND AIMS

The gene flow through pollen or seeds governs the extent of spatial genetic structure in plant populations. Another factor that can contribute to this pattern is clonal growth. The perennial species Arabidopsis lyrata ssp. petraea (Brassicaceae) is a self-incompatible, clonal species found in disjunctive populations in central and northern Europe.

METHODS

Fourteen microsatellite markers were employed to study the level of kinship and clonality in a high-altitude mountain valley at Spiterstulen, Norway. The population has a continuous distribution along the banks of the River Visa for about 1.5 km. A total of 17 (10 m x 10 m) squares were laid out in a north-south transect following the river on both sides.

KEY RESULTS

It is shown that clonal growth is far more common than previously shown in this species, although the overall size of the genets is small (mean diameter = 6.4 cm). Across the whole population there is no indication of isolation by distance, and spatial genetic structure is only visible on fine spatial scales. In addition, no effect of the river on the spatial distribution of genotypes was found.

CONCLUSIONS

Unexpectedly, the data show that populations of small perennials like A. lyrata can behave like panmictic units across relatively large areas at local sites, as opposed to earlier findings in central Europe.

Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes

Although many properties of spatial autocorrelation statistics are well characterized, virtually nothing is known about possible correlations among values at different spatial scales, which ultimately would influence how inferences about spatial genetics are made at multiple spatial scales. This article reports the results of stochastic space-time simulations of isolation by distance processes, having a very wide range of amounts of dispersal for plants or animals, and analyses of the correlations among Moran's I-statistics for different mutually exclusive distance classes. In general, the stochastic correlations are extremely large (>0.90); however, the correlations bear a complex relationship with level of dispersal, spatial scale and spatial lag between distance classes. The correlations are so large that any existing or conceived statistical method that employs more than one distance class (or spatial scale) should not ignore them. This result also suggests that gains in statistical power via increasing sample size are limited, and that increasing numbers of assayed loci generally should be preferred. To the extent that sampling error for real data sets can be treated as white noise, it should be possible to account for stochastic correlations in formulating more precise statistical methods. Further, while the current results are for isolation by distance processes, they provide some guidance for some more complex stochastic space-time processes of landscape genetics. Moreover, the results hold for several popular measures other than Moran's I. In addition, in the results, the signal to noise ratios strongly decreased with distance, which also has several implications for optimal statistical methods using correlations at multiple spatial scales.

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.

Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal

We present a study of fine-scale spatial genetic structure (SGS) and assess the impact of seed and pollen dispersal on the pattern of genetic diversity in the predominantly selfing Hordeum spontaneum. The study included (1) direct measurement of dispersal in a controlled environment, and (2) analyses of SGS and estimation of the ratio of pollen to seed flow in three natural populations sampled in linear transects at fixed increasing inter-plant distances. Analysis of SGS with 10 nuclear SSRs showed in all three populations a significant autocorrelation for the distance classes of 1 or 2 m and a negative linear relationship between kinship coefficients, calculated for pairs of individuals, and logarithm of geographical distance between members of the pairs. Major seed dispersal (95%) was found to be within 1.2 m from the mother plant. Pollen flow, estimated from the comparison of nuclear and chloroplast variation, was spatially limited as much as was seed dispersal, and tended to be overestimated when measured at spatial scales exceeding that of SGS. We conclude that combined effects of selfing, occasional outcrossing, localized seed dispersal and high plant density create an equilibrium between drift and gene flow in this species resulting in SGS at a very fine spatial scale.

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands

The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa.

Contrasting impacts of pollen and seed dispersal on spatial genetic structure in the bird-pollinated Banksia hookeriana

In plants, pollen- and seed-dispersal distributions are characteristically leptokurtic, with significant consequences for spatial genetic structure and nearest-neighbour mating. However, most studies to date have been on wind- or insect-pollinated species. Here, we assigned paternity to quantify effective pollen dispersal over 9 years of mating, contrasted this to seed dispersal and examined their effects on fine-scale spatial genetic structure, within the bird-pollinated shrub Banksia hookeriana (Proteaceae). We used 163 polymorphic amplified fragment length polymorphism markers to assess genetic structure and pollen dispersal in a spatially discrete population of 112 plants covering 0.56 ha. Spatial autocorrelation analysis detected spatial genetic structure in the smallest distance class of 0-5 m (r=0.025), with no significant structure beyond 8 m. Experimentally quantified seed-dispersal distances for 337 seedlings showed a leptokurtic distribution around a median of 5 m, reaching a distance of 36 m. In marked contrast, patterns of pollen dispersal for 274 seeds departed strikingly from typical near-neighbour pollination, with a distribution largely corresponding to the spatial distribution of plants. We found very high multiple paternity, very low correlated paternity and an equal probability of siring for the 50 closest potential mates. Extensive pollen carryover was demonstrated by multiple siring in 83 of 86 (96.5%) two-seeded fruits. Highly mobile nectar-feeding birds facilitate this promiscuity through observed movements that were effectively random. As the incidence of bird-pollination is markedly greater in the Southwest Australian Floristic Region than elsewhere, our results have broad and novel significance for the evolution and conservation for many species in Gondwanan lineages.