Shortest Distance Class Research Articles

Patterns of genetic diversity, spatial genetic structure and gene flow in Campomanesia xanthocarpa: insights from SSR markers of different genomic origins.

Campomanesia xanthocarpa (Mart.) O. Berg is a South American fruit tree species with important ecological and medicinal properties, which remnants are currently found mainly in isolated forest fragments. In this study, SSR markers from three different genomic origins (gene-linked, nuclear neutral, and organellar) were used to evaluate the patterns of genetic diversity, fine-scale spatial genetic structure and historical gene flow in fragmented forest formations of C. xanthocarpa from the Atlantic Forest in southern Brazil. Our results show that the forest fragments present moderate to high levels of genetic diversity in comparison to species presenting similar life traits, although a trend opposite to expected was observed concerning gene-linked and neutral SSR markers. The fine-scale spatial genetic structure revealed different patterns in short and large distance classes, with a distinct influence of gene-linked and neutral markers in driving the genetic structure in each distance class. The presence of an isolation-by-adaptation pattern implies the need for maintenance of the current remnants to assure the conservation of the private alleles. Finally, as the genetic diversity is found predominantly within forest fragments, programs of seed collection and/or genetic rescue should prioritize a larger number of individuals within each fragment, to increase the sampled diversity.

Clone Configuration and Spatial Genetic Structure of Two Halophila ovalis Populations With Contrasting Internode Lengths

Fine-scale spatial genetic structure (SGS) is predominantly determined by gene flow. While sexually reproducing plants can disperse their genes through pollen and seed grains, clonal plants can additionally disperse genes through clonal growth. Plants’ clonal reproduction strategy, however, often varies within and between species. Still, the effect of differential clonal reproduction strategy on fine-scale SGS remains somewhat unclear. Halophila ovalis is a fast-growing clonal seagrass, whose internode length (which defines a species’ clonal reproduction strategy) varies among populations. Using eight polymorphic microsatellites, here we compare the genetic diversity, clonal structure and fine-scale SGS of two H. ovalis populations with contrasting internode lengths (Yingluo versus Xialongwei populations). We found moderate to high genotypic and allelic richness and heterozygosities in both populations. Compared to Xialongwei population, genetic and genotypic diversity was significantly lower in Yingluo population. Although their internode length was relatively short, clones of Yingluo population spread farther than those of Xialongwei population. Sexual-to-vegetative dispersal variance ratios were 34.6 and 445.5 in Yingluo and Xialongwei populations, respectively. In both populations, clonal growth significantly intensified the SGS, especially in short distance classes. The SGS at small distance classes were weaker in Yingluo than Xialongwei, in part, due to more intermingled distribution of genets and more extensive clonal expansion in the former population. Our results indicate that vegetative dispersal variance/distance, rather than internode length, plays a crucial role in shaping the fine-scale genetic structure.

Population genetics and fine-scale genetic structure of Rhizopogon roseolus in the Tottori sand dune

We investigated the population genetics and fine-scale genetic structure of Rhizopogon roseolus. A total of 173 R. roseolus sporocarps were collected from two stands in the Tottori sand dune. We developed and applied five novel polymorphic microsatellite (SSR; simple sequence repeat) markers for sporocarp genotyping. In total, we identified 110 genets, most of which were small in size. Spatial autocorrelation analyses revealed a significantly positive genetic structure in short-distance classes. The inbreeding coefficient value was significant in both stands (FIS = 0.18), while the FST value (FST = 0.020) indicated little genetic differentiation between the two populations. The majority of alleles were distributed in both stands with similar frequencies. These results suggest that short-distance spore dispersal plays a dominant role in generating new genets, and eventually increases the frequency of inbreeding in the Tottori sand dune, whereas rare gene flow between the two stands, possibly associated with spore dispersal by mycophagous animals, could reduce genetic differentiation.

Genet dynamics and ecological functions of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji

To understand the reproduction of the pioneer ectomycorrhizal fungi Laccaria amethystina and Laccaria laccata in a volcanic desert on Mount Fuji, Japan, the in situ genet dynamics of sporocarps were analysed. Sporocarps of the two Laccaria species were sampled at fine and large scales for 3 and 2 consecutive years, respectively, and were genotyped using microsatellite markers. In the fine-scale analysis, we found many small genets, the majority of which appeared and disappeared annually. The high densities and annual renewal of Laccaria genets indicate frequent turnover by sexual reproduction via spores. In the large-scale analysis, we found positive spatial autocorrelations in the shortest distance class. An allele-clustering analysis also showed that several alleles were distributed in only a small, localised region. These results indicate that Laccaria spores contributing to sexual reproduction may be dispersed only short distances from sporocarps that would have themselves been established via rare, long-distance spore dispersal. This combination of rare, long-distance and frequent, short-distance Laccaria spore dispersal is reflected in the establishment pattern of seeds of their host, Salix reinii.

Effects of Reduced Impact Logging on genetic diversity and spatial genetic structure of a Hymenaea courbaril population in the Brazilian Amazon Forest

Levels of genetic diversity, inbreeding, and spatial genetic structure were investigated at different ontogenic stages for a population of Hymanaea courbaril, before and after Reduced Impact Logging (RIL) was applied, in a 546-ha plot in the Tapajós National Forest, in the Brazilian Amazon. The multilocus genotype of nine microsatellites loci was determined for 74 juveniles (dbh < 10 cm), 59 subadults (10 ≤ dbh < 50 cm), 76 adults (50 ≤ dbh < 100 cm), and 54 large adult trees (dbh ≥ 100 cm). The results show a clear tendency of increase in the levels of observed heterozygosity and decrease in the fixation index between juveniles and large adult trees. Although these results were not significant ( t-test, P > 0.05), they suggest the occurrence of inbreeding depression. All ontogenic stages showed spatial genetic structure at short distance classes (<200 m), but the levels are not constant among the subpopulations. The harvest of 61% of the reproductive trees caused a loss of 37 (25%) low frequency and rare alleles from the mature population. However, 24 of the “lost” alleles are present in juvenile and subadult populations which might allow their reintroduction into the population when these trees become reproductive. RIL also caused a reduction of the observed and expected heterozygosity of the unlogged reproductive population in comparison to the reproductive population, although these results were not statistically significant ( t-test, P > 0.05). Logging also reduced the distance of the spatial genetic structure in the reproductive population from about 800 to 200 m. In general, our results indicate that RIL affected the gene pool and spatial genetic structure of the reproductive population.

EFFECTS OF KIN-STRUCTURED SEED DISPERSAL ON THE GENETIC STRUCTURE OF THE CLONAL DIOECIOUS SHRUB ILEX LEUCOCLADA

Nonrandom patterns of gene dispersal have been identified as possible causes of genetic structuring within populations. Attempts to model these patterns have generally focused solely on the effects of isolation by distance, but the processes involved are more complex than such modeling suggests. Here, we extend considerations of gene dispersal processes beyond simple isolation by distance effects by directly evaluating the effects of kin-structured gene dispersal mediated by the group dispersal of related seeds within fruits (i.e., kin-structured seed dispersal) by birds on genetic structure in Ilex leucoclada, a clonal dioecious shrub. To examine the genetic structure patterns, we established two 30x30 m plots (one with immature soils in old-growth forest and one in secondary forest, designated IM and SC, respectively) with different I. leucoclada stem densities. In these two plots 145 and 510 stems were found, representing 78 and 85 genets, respectively, identified by analyzing their genotypes at eight microsatellite loci. The clonal structure was stronger in the SC plot than in the IM plot. Correlograms of coancestry for genets in both plots exhibited significant, positive, high values in the shortest distance class, indicating the presence of strong genetic structure. However, Sp statistics revealed that the pattern of the genetic structure differed between the plots. In addition, to estimate the family structure within fruits, we sampled forty fruits, in total, from 15 randomly selected plants in the area around the IM and SC plots, and found that 80% of the fruits were multiseeded and 42-100% of the multiseeded fruits contained at least one pair of full sibs. Simulations based on these estimates demonstrated that the group dispersal of related seeds produced through correlated mating both within and across fruits, but not unstructured half-sib dispersal, could generate the observed magnitude and trends of genetic structure found in the IM plot. Furthermore, in addition to kin-structured seed dispersal, isolation by distance processes is also likely to promote genetic substructuring in the SC plot. After discussing possible ecological factors that may have contributed to the observed genetic structure, we contrast our results with those predicted by general isolation by distance models, and propose that kin-structured seed dispersal should promote some evolutionary phenomena, and thus should be incorporated, where appropriate, in models of gene dispersal in natural plant populations.

Effects of canopy gaps on the genetic structure of Camellia japonica saplings in a Japanese old-growth evergreen forest

The genetic structure of Camellia japonica saplings was investigated in relation to canopy conditions in an old-growth evergreen forest in Tsushima, Japan. To elucidate effects of canopy gaps on genetic structure, a 1 ha study site was divided into 20 x 20 m quadrats, which were classified into a gap quadrats (GAP), closed canopy quadrats (CLS) and mixed quadrats. Five GAP quadrats and six CLS quadrats were analyzed separately. Isolation-by-distance was tested by examining the correlation between genetic distance and geographic distance. A significant positive correlation was detected for GAP quadrats, whilst that for CLS quadrats was significantly smaller and not significantly different from zero. On the other hand, an analysis using Moran's I spatial autocorrelation coefficients indicates that the genetic structure is weaker in GAP quadrats than in CLS quadrats in short distance classes. The values were significantly positive for both types of quadrat. These results, along with our field observations on flowering, suggest that canopy gaps affect the genetic structure of C. japonica saplings in two distinct ways. First, canopy gaps may promote flowering and mating in an isolation-by-distance manner within canopy gaps. Second, canopy gaps may promote seed production and resulting overlap in seed shadows may weaken fine-scale genetic structures.

Stem distribution and clonal structure of Chamaecyparis pisifera growing in an old‐growth beech‐conifer forest

To elucidate sapling patch formation and the mode of regeneration occurring in Chamaecyparis pisifera, we investigated stem distribution and clonal structure of this species in an old‐growth beech‐conifer forest in central Japan. The study was carried out in a 1‐ha plot using small and large sapling (d.b.h. &lt;5 cm, 0.5 m ≤ height &lt; 2 m and d.b.h. &lt; 5 cm, height ≥ 2 m, respectively) and adult (d.b.h. ≥5 cm) stems of Chamaecyparis pisifera. The numbers of small and large sapling stems were 677 and 149 in the plot, respectively, and they were strongly aggregated. Adult stems occurred at much lower density (90 stems in the plot) and were weakly clustered. Fifty multilocus genotypes at nine allozyme loci were detected among sampled stems. Small and large sapling stems with identical genotypes showed aggregated distribution, while some neighboring adult stems had the same genotypes. Spatial autocorrelation of alleles in small and large sapling stems revealed a strongly positive association among stems within a distance of 10 m; but a negative association as distance increased. In adult stems, a strongly positive value was found only in the shortest distance class. These results indicate that clonal growth by layering occurred at the sapling stage and contributed to patch formation. Our results also suggest that the clonal growth by layering is ecologically significant throughout the life history of Chamaecyparis pisifera, particularly as an important strategy for the sapling establishment in the early stage of regeneration process.

Spatial analysis of allozyme and microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae).

The genetic structure of the land snail Helix aspersa was investigated for 21 populations collected along a road located in the polders of the Bay of Mont-Saint-Michel (Brittany, France), following a sampling scheme the area of which did not exceed 900 m in length. A total of 369 individuals were genotyped for five enzymatic markers and seven microsatellite loci. We used sequential hierarchical F-statistics at different spatial scales and spatial autocorrelation statistics to explore recent historical patterns involved in the observed genetic distribution. Whatever the statistics used, congruent levels of spatial genetic substructuring across loci were demonstrated, excepted for one allozyme locus. Overall spatial genetic arrangement matched in a substantial fashion theoretical predictions based on the limited dispersal power of land snails. Positive autocorrelation over short-distance classes may result from the development of genetically distinct patches of individuals organized in family-structured colonies. Therefore, spatial signatures of average I correlograms can be viewed as the expression of a stepping-stone model of population structure, sometimes involving external migrational events. Overall, the revealed pattern of population subdivision on a microgeographical scale was suggestive of a neighbourhood structure. Finally, microsatellite loci are especially suitable for the detection of small genetic clustering, and combining different classes of markers offers the potential to gain further insight into the description of spatial genetic variability over short temporal and geographical scales.

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.

Differences in genetic structure between two Japanese beech (Fagus crenata Blume) stands.

To examine the effects of forest cutting on within-population genetic structure, the genetic structure and variability of two Japanese beech (Fagus crenata Blume) stands with contrasting histories in relation to cutting were investigated. Six hundred and sixty beech trees, covering two hectares in total, were mapped and genetically analysed using nine isozyme loci encoding eight enzyme systems. The proportion of polymorphic loci, the average number of alleles per locus, the effective number of alleles per locus, the expected heterozygosity and the observed heterozygosity were 78, 3.3, 1.31, 0.200 and 0.189, respectively, in a secondary stand (designated AK) cut during the 1920s. Corresponding figures were 78, 3.3, 1.33, 0.203 and 0.193, respectively, in a primary stand designated KU. The inbreeding coefficient and the grand mean of the number of alleles in common (NAC) were 0.055 and 1.684 in AK, and 0. 042 and 1.649 in KU, respectively. The genetic variability was slightly but significantly lower in AK. The genetic structure of the two stands was strikingly different. The proportions of positively significant Moran's I and SND values found in the shortest distance class were 0.86 and 0.38 for AK, and 0.14 and 0.29 for KU, respectively. Furthermore, significant linkage disequilibrium was observed in AK, but none at all in KU. To examine which, if any, differences in the genetic structure would be likely to influence succeeding generations, we simulated a self-thinning process. The simulation suggested that reduced genetic variability and linkage disequilibrium would have significant influence in the AK stand for several generations.

Genetic structure within a Japanese stone pine (Pinus pumila regel) population on Mt. Aino-dake in central Honshu, Japan

In previous investigations, natural layering of Japanese stone pine (Pinus pumila) was suggested by the occurrence of adventitious roots. However, there is no genetic evidence so far that this species actually produces offspring by natural layering. We, therefore, investigated clonal structure and spatial genetic structure within a 38×18 m plot on Mt. Aino-dake, using allozyme, random amplified polymorphic DNA (RAPD), and inter-simple sequence repeat (ISSR) analyses. We found 24 genets, with stems found to be genetically identical in multiple tests, which extended later-ally against the direction of the slope, indicating that there were clonal structures originating from elongation of ramified stems and subsequent natural layering. The results suggest, however, that less than one third of the 200 stems analyzed from this site were clonaly propagated. We also analyzed spatial genetic structure by spatial autocorrelation. Many of the spatial autocorrelation coefficients were significantly positive in short distance classes. We concluded that the species has genetic structures which largely originate from clonal propagation and avian seed dispersal.

Spatial structure of genetic variation in a population of the endangered plant Cerastium fischerianum var. molle (Caryophyllaceae).

The spatial genetic structure within a population of an endangered plant, Cerastium fischerianum var. molle, was examined using spatial autocorrelation analysis. All individuals in 22 × 15 m area in a population were mapped and genotyped by three allozyme loci. Many spatial autocorrelation indices (Moran's I) were significantly larger than the expected values and their averages across three marker loci examined were positive in the short distance classes and the opposite pattern was shown in the larger distance classes, suggesting that individuals located nearly each other tend to have similar genotypes and pairs of individuals located far from each other tend to have different genotypes. Because the marker loci are considered to be neutral and the linkage disequilibria were not detected, the spatial genetic structure observed in this study seems to result from the restricted gene flow because of predominant selfing of C. fischerianum var. molle.

Spatial Autocorrelation of Genotypes in a Gynodioecious Population of Chionographis japonica var. kurohimensis (Liliaceae)

The spatial structure of allele frequencies for three polymorphic enzyme loci was examined in a gynodioecious population of Chionographis japonica var. kurohimensis. Spatial autocorrelation indices (Moran's I) were significantly larger in the shortest distance class than expected value, indicating that genetic similarity is shared among near-neighbor individuals. Because spatial patterns of the three loci examined showed a similar pattern, and significant linkage disequilibrium was not found among pairwise combinations of these loci, the population substructure detected in this study probably resulted from restricted gene flow because of predominant selfing in the hermaphrodites.