Significant Fine-scale Spatial Genetic Structure Research Articles

Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum

Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.

Directional seed and pollen dispersal and their separate effects on anisotropy of fine-scale spatial genetic structure among seedlings in a dioecious, wind-pollinated, and wind-dispersed tree species, Cercidiphyllum japonicum.

Prevailing directions of seed and pollen dispersal may induce anisotropy of the fine‐scale spatial genetic structure (FSGS), particularly in wind‐dispersed and wind‐pollinated species. To examine the separate effects of directional seed and pollen dispersal on FSGS, we conducted a population genetics study for a dioecious, wind‐pollinated, and wind‐dispersed tree species, Cercidiphyllum japonicum Sieb. et Zucc, based on genotypes at five microsatellite loci of 281 adults of a population distributed over a ca. 80 ha along a stream and 755 current‐year seedlings. A neighborhood model approach with exponential‐power‐von Mises functions indicated shorter seed dispersal (mean = 69.1 m) and much longer pollen dispersal (mean = 870.6 m), effects of dispersal directions on the frequencies of seed and pollen dispersal, and the directions with most frequent seed and pollen dispersal (prevailing directions). Furthermore, the distance of effective seed dispersal within the population was estimated to depend on the dispersal direction and be longest at the direction near the prevailing direction. Therefore, patterns of seed and pollen dispersal may be affected by effective wind directions during the period of respective dispersals. Isotropic FSGS and spatial sibling structure analyses indicated a significant FSGS among the seedlings generated by the limited seed dispersal, but anisotropic analysis for the seedlings indicated that the strength of the FSGS varied with directions between individuals and was weakest at a direction near the directions of the most frequent and longest seed dispersal but far from the prevailing direction of pollen dispersal. These results suggest that frequent and long‐distance seed dispersal around the prevailing direction weakens the FSGS around the prevailing direction. Therefore, spatially limited but directional seed dispersal would determine the existence and direction of FSGS among the seedlings.

Genetic tracking of density‐dependent adult recruitment: A case study in a subtropical oak

Abstract Density‐dependent recruitment is fundamental to understanding species diversity and community dynamics in plants. Although there is compelling evidence that seeds and seedlings die from conspecific negative density dependence (CNDD) as predicted by the Janzen–Connell hypothesis, characterising adult recruitment remains a challenge for long‐living trees. Previous studies have used the decrease in fine‐scale spatial genetic structure (FSGS) across life stages to indicate CNDD; however, this has not been tested rigorously. We addressed these challenges by integrating dispersal kernels and FSGS. To establish links between density dependence and FSGS, we simulated seedlings based on the estimated dispersal kernels from parentage analyses, and further simulated adults under various seedling‐to‐adult recruitment scenarios, using an individual‐based spatially explicit model. We tested this method in an isolated Cyclobalanopsis glauca population on China's Dajinshan Island. We detected significant FSGS in the seedlings and weaker, though also significant, FSGS in the adults. As expected, the observed FSGS of seedlings was well predicted by the simulated seedlings, with observations falling inside the 95% confidence envelopes over all distance classes. However, the simulations showed that CNDD enhanced the FSGS while positive density dependence dampened it during the seedling‐to‐adult transition. The adult FSGS of our population was therefore explained by positive rather than negative density‐dependent adult recruitment. Synthesis. Our study demonstrates that the change of FSGS in conjunction with dispersal‐based model tests can offer a valuable insight into density‐dependent adult recruitment. The results indicate that the transitions from seedlings to adults in C. glauca are dominantly regulated not by Janzen–Connell effects, but by processes of positive density dependence. More broadly, the findings may provide a caution against extrapolations of widespread Janzen–Connell effects in seeds and seedlings to adult recruits, underscoring a critical gap between mechanisms at early stages and long‐term population and community dynamics.

Fine-scale spatial genetic structure and intra-specific interactions of Populus nigra within a natural river corridor along the lower Allier River (France)

Spatial genetic structure (SGS) studies contribute to our understanding of gene flow and species dispersal. Only a few studies have linked the spatio-temporal pattern of SGS and intra-specific interactions. Black poplar (Populus nigra L.) is a threatened pioneer riparian tree species along many rivers across Europe. We studied its SGS in cohorts of varying ages at a fine-scale (i.e. at distances including the zone of influence between individuals) to better understand local patterns of dispersal and intra-specific interactions during early life-stages. We genotyped 349 P. nigra individuals in three gravel bars along a 1.6 km reach of the Allier River in the Réserve Naturelle du Val d'Allier, central France. We found high genetic diversity values (He = 0.860) thus identifying this site as important for the conservation of P. nigra genetic diversity. We also found significantly more clones in locations exposed to the river flow compared with less exposed locations. These clones offer mechanical protection and habitat improvement (through facilitation) to individuals in close proximity. A significant fine-scale SGS was observed in the youngest cohort at the gravel bar scale while none was observed in the older cohorts or at the river reach scale. This pattern was confirmed by a reanalysis of published data on the Garonne River. A shift in intra-specific interactions, from facilitation to competition through self-thinning, could explain the loss of SGS in older cohorts. This highlights the importance of shifts in intraspecific interactions through life and their consequence on population genetic structure.

Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus species

Abstract Understanding the impact of management on the dispersal potential of forest tree species is pivotal in the context of global change, given the implications of gene flow on species evolution. We aimed to determine the effect of logging on gene flow distances in two Nothofagus species from temperate Patagonian forests having high ecological relevance and wood quality. Therefore, a total of 778 individuals (mature trees and saplings) of Nothofagus alpina and N. obliqua, from a single plot managed 20 years ago (2.85 hectares), were mapped and genotyped at polymorphic nuclear microsatellite loci. Historical estimates of gene dispersal distance (based on fine-scale spatial genetic structure) and contemporary estimates of seed and pollen dispersal (based on spatially explicit mating models) were obtained. The results indicated restricted gene flow (gene distance ≤ 45 m, both pollen and seed), no selfing and significant seed and pollen immigration from trees located outside the studied plot but in the close surrounding area. The size of trees (diameter at breast height and height) was significantly associated with female and/or male fertility. The significant fine-scale spatial genetic structure was consistent with the restricted seed and pollen dispersal. Moreover, both estimates of gene dispersal (historical and contemporary) gave congruent results. This suggests that the recent history of logging within the study area has not significantly influenced on patterns of gene flow, which can be explained by the silviculture applied to the stand. The residual tree density maintained species composition, and the homogeneous spatial distribution of trees allowed the maintenance of gene dispersal. The short dispersal distance estimated for these two species has several implications both for understanding the evolution of the species and for defining management, conservation and restoration actions. Future replication of this study in other Nothofagus Patagonian forests would be helpful to validate our conclusions.

Spatial genetic structure within a population of nine-banded armadillos in western Mississippi

AbstractThe nine-banded armadillo (Dasypus novemcinctus) is unique among mammals because females produce litters of genetically identical quadruplets via monozygotic polyembryony. This unusual form of reproduction could have profound impacts on the spatial genetic structure of populations of armadillos, but at present it is unclear whether littermates remain together as adults, or if sex-biased dispersal occurs. The goal of our study was to determine whether fine-scale spatial genetic structure (FSGS) within a population of armadillos diminishes with age (i.e., from juvenile to adult due to the dispersal of littermates away from one another), and if the degree of FSGS for a given age class differs between the sexes. We obtained genotype data at seven microsatellite DNA loci for 421 individuals in a wild population of armadillos inhabiting the Yazoo National Wildlife Refuge in western Mississippi. Correlogram analyses based on measures of spatial genetic autocorrelation showed weak but significant FSGS that was driven by positive spatial genetic autocorrelation among both male and female juveniles and adult males, but not adult females. Positive spatial genetic autocorrelation among adult males could be due to either female-biased dispersal or high variance in male reproductive success. Further work is required to discriminate between these two possibilities.

Distinctions in Fine-Scale Spatial Genetic Structure Between Growth Stages of Picea jezoensis Carr.

Conifers in northern forests, such as fir and spruce, preferably regenerate on coarse woody debris, including fallen logs, stumps, and snags. In northern Japan, the sub-boreal conifer species Picea jezoensis is completely dependent on coarse woody debris for seedling establishment. To understand the fine-scale spatial genetic structure (FSGS) of this species, a 5-ha plot was established in central Hokkaido, and 531 individual trees were categorized into four life-stages (seedling, sapling, juvenile, and mature) on the basis of age and size. The FSGS of the established seedlings and later growth stages was investigated using 11 nuclear simple sequence repeat loci. A STRUCTURE analysis of seedlings and saplings established on fallen logs revealed that genetically related individuals were spatially localized between adjacent logs. We also found a significant FSGS in early life-stages based on a decline in the kinship coefficient calculated between individuals over shorter to longer spatial distances. Furthermore, the estimation of dispersal kernels indicated the frequent occurrence of short-distance seed dispersal. These results indicated that genetically related seedlings and saplings regenerated on the same or nearby fallen logs. In contrast to the results for the early stages, mature-stage trees showed no significant FSGS. We ran a simulation to examine the hypothesis that the FSGS could be eliminated by demographic thinning during life history processes. We calculated values for simulated offspring generated under three sets of conditions; i.e., by removing (i) inbred individuals, (ii) randomly chosen individuals, and (iii) all individuals on the specific fallen logs. However, the results for the FSGS were significant for all simulated data sets. This indicated that inbreeding depression, stochastic loss, or eradication of establishment sites by local disturbances alone could not explain the lack of FSGS among mature-stage trees. Therefore, it is possible that the colonization history of mature trees present on the study site might differ from that of the current offspring.

Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species.

Genetic responses to environmental changes take place at different spatial scales. While the effect of environment on the distribution of species' genetic diversity at large geographical scales has been the focus of several recent studies, its potential effects on genetic structure at local scales are understudied. Environmental effects on fine-scale spatial genetic structure (FSGS) were investigated in four Alpine conifer species (five to eight populations per species) from the eastern Italian Alps. Significant FSGS was found for 11 of 25 populations. Interestingly, we found no significant differences in FSGS across species but great variation among populations within species, highlighting the importance of local environmental factors. Interannual variability in spring temperature had a small but significant effect on FSGS of Larix decidua, probably related to species-specific life history traits. For Abies alba, Picea abies and Pinus cembra, linear models identified spring precipitation as a potentially relevant climate factor associated with differences in FSGS across populations; however, models had low explanatory power and were strongly influenced by a P.cembra outlier population from a very dry site. Overall, the direction of the identified effects is according to expectations, with drier and more variable environments increasing FSGS. Underlying mechanisms may include climate-related changes in the variance of reproductive success and/or environmental selection of specific families. This study provides new insights on potential changes in local genetic structure of four Alpine conifers in the face of environmental changes, suggesting that new climates, through altering FSGS, may also have relevant impacts on plant microevolution.

Genetic structure and internal gene flow in populations of Schinus molle (Anacardiaceae) in the Brazilian Pampa

One of the most important aspects for population ecology and evolution is to understand the connectivity between individuals and their groups. In this study, amplified fragment length polymorphism (AFLP) markers were employed aiming to examine genetic diversity, spatial genetic structure, and internal gene flow of nine populations of Schinus molle across the Brazilian Pampa. The dispersal capacity of S. molle in the Brazilian Pampa, the implications of the forest fragmentation to species genetic structure, and the impact of the actual genetic structure of the species to its conservation and management were investigated. AFLP markers revealed low genetic diversity and clear genetic structure among populations. Significant fine-scale spatial genetic structure at short distances was observed in all populations. Estimates of gene dispersal distance suggest that the dispersion capacity of this species is larger than the area covered by the studied populations. However, fragmentation hampers the gene flow among populations. The management of S. molle natural occurrence in this biome seems to be simple considering the species plasticity. The conservation of the species genetic resource depends on maintaining the extant forest patches and promoting their connectivity.

Fine scale spatial genetic structure of the endangered Heptacodium miconioides endemic to China

Abstract A study on the spatial genetic structure of endangered plants can provide basic information to support species management and conservation. Heptacodium miconioides Rehder is an endangered plant endemic to China. The fine-scale spatial genetic structure of H. miconioides individuals and within population age classes was studied to elucidate population history and selection pressures and to predict the species evolutionary potential. Significant fine-scale spatial genetic structure of H. miconioides populations at a distance less than 8.06 m may occur because of limited pollen dispersal, asexual reproduction and micro-environmental selection. The significant fine-scale spatial genetic structure of H. miconioides populations from four different age classes might be due to self-thinning and human disturbance.

Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)

Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (H(E) : 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults R(S) : 3.91; juveniles R(S) : 2.83) and observed heterozygosity than adult trees (adults H(O) : 0.62; juveniles H(O) : 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to miss-management of genetic resources and population fragmentation.

Determinants of fine-scale spatial genetic structure in three co-occurring rain forest canopy trees in Borneo

Fine-scale spatial genetic structure (FSGS) within plant populations is an emergent property of the recruited adult trees, influenced by pollen and seed mediated gene flow, selection and demographic processes. This study aims to increase our understanding of the individual species traits that contribute to the generation of FSGS in the Dipteropcarpaceae, which is an ecologically and economically important family of tropical trees that dominate lowland forests in Southeast Asia. We examined FSGS in three cooccurring dipterocarp species at a single site in Borneo. Shorea xanthophylla, Parashorea tomentella and Dipterocarpus grandiflorus share limited seed dispersal but differ markedly in flower size, pollinator body size and pollen dispersal. Here we explore the role of pollen dispersal limitation in shaping FSGS in these three species. Using six microsatellite loci, we explore patterns of FSGS and landscape genetic structure and compare these across species. Significant FSGS was observed in S. xanthophylla and P. tomentella, both of which are known to have relatively limited pollen dispersal, but no clear signal of FSGS was observed in D. grandiflorus. Significantly greater FSGS was observed in P. tomentella (Sp = 0.012) than S. xanthophylla (Sp = 0.007) despite greater pollen dispersal in P. tomentella. Bayesian clustering analysis revealed significant structure in P. tomentella at the scale of the forest reserve (4000 ha). We discuss the alternative explanations for the observed patterns of FSGS emphasising the complexity of the mechanisms that can generate FSGS in long-lived trees. The extent of species-specific pollen dispersal is one factor that can contribute to differences in FSGS across species, but is not the only determinant. The observed patterns of FSGS and landscape scale genetic structure in S. xanthophylla and P. tomentella illustrate the potential of gap regeneration to counter act pollen dispersal and contribute to increased aggregation of related individuals (FSGS). © 2010 Elsevier GmbH. All rights reserved.

Biological Flora of the British Isles: Primula vulgaris Huds. (P. acaulis (L.) Hill)

1. This account presents information on all aspects of the biology of Primula vulgaris Huds. (Primrose) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characteristics, herbivores and disease, history and conservation. 2. Primula vulgaris is a native perennial herb with a very wide distribution in the British Isles. In many lowland areas it is essentially a plant of woodlands and hedgerows, although in the west it can occur abundantly in grasslands and other communities such as heaths. In northern and western Britain and Ireland, it may be frequent in open and even exposed habitats. Its distribution is linked with soil moisture and atmospheric humidity. It is shade tolerant, but it flowers most profusely in canopy gaps. 3. Primula vulgaris is a rosette hemicryptophyte that reproduces mainly through seeds. Vegetative spread is restricted and only occurs within very short distances from the mother plant through the production of lateral rosettes. Although individual rosettes may die, plants are relatively long-lived (life expectancy of a newborn individual: 48.3 years). The mean age at first flowering was 20 months. 4. Pollination is mainly by bumblebees and other bees, but other long-tongued pollinators including syrphids, bee-flies and even butterflies may be locally important. P. vulgaris is an obligate outbreeder, with two genetically determined self-incompatible morphs ('pin' and 'thrum'). A third morph ('homostyle' or 'long homostyle'), with a stigma like that of pin but anthers like that of thrum, has been found in Somerset and North Dorset. In years when pollinators are scarce, homostyles have higher reproductive success than pins and thrums, suggesting that reproductive assurance could have had a profound effect on the evolution of homostyly in P. vulgaris. 5. Seeds are dispersed by ants and rodents. Dispersal is usually restricted to a few centimetres or decimetres from maternal plants, resulting in significant fine-scale spatial genetic structure and small neighbourhood sizes. Pollen flow, on the other hand, is more extensive, but still limited to a few metres from paternal plants. 6. Populations of P. vulgaris have not changed markedly during the last century in most parts of Britain and Ireland and it is not threatened with extinction nationally. However, there is evidence that Primroses were formerly more widespread and have decreased with the decline of coppicing and pollarding. In East Anglia, woodland populations have declined greatly in response to a series of hot, dry summers since 1970. Small, isolated populations of P. vulgaris often show reduced reproductive success, potentially affecting their long-term survival. Preservation of local habitat conditions and restoration of gene flow among populations are required to maintain viable populations of P. vulgaris in the long term.

Multigenerational analysis of spatial structure in the terrestrial, food‐deceptive orchid Orchis mascula

Summary In long‐lived, terrestrial orchids, strong aggregation of adults and recruits within populations and pronounced spatial association between recruits and adults can be expected when seed dispersal is limited, probabilities of seed germination decrease with increasing distance from mother plants and/or not all mother plants contribute to future generations. When individuals are distributed evenly across life‐history stages, these processes can also be expected to result in a significant fine‐scale spatial genetic structure in recruits that will persist into the adult‐stage class. We combined detailed spatial genetic and point pattern analyses across different generations with parentage analyses to elucidate the role of the diverse processes that might determine spatial structure in Orchis mascula. Analyses of spatial point patterns showed a significant association between adults and recruits and similar clustering patterns for both. Weak, but highly significant spatial genetic structure was observed in adults and recruits, but no significant differences were observed across life stages, indicating that the spatial genetic structure present in recruits persists into the adult stage. Parentage analyses highlighted relatively short seed dispersal distances (median offspring‐recruitment distance: 1.55 and 1.70 m) and differential contribution of mother plants to future generations. Persistence of fine‐scale spatial genetic structure from seedlings into the adult stage class is consistent with the life history of O. mascula, whereas relatively large dispersal distances of both pollen and seeds compared to the fine‐scale clustering of adults and seedlings suggest overlapping seed shadows and mixing of genotypes within populations as the major factors explaining the observed weak spatial genetic structure. Nonetheless, comparison of the spatial association between recruits and adults with the genetic analysis of offspring‐parent distances suggests that the tight clustering of recruits around adults was probably caused by decreasing probabilities of seed germination with increasing distance from mother plants. Synthesis. This study shows that the approach presented here, which combines spatial genetic and spatial pattern analyses with parentage analyses, may be broadly applied to other plant species to elucidate the processes that determine spatial structure within their populations.

Inferring establishment histories in populations of Quercus dentata (Fagaceae) from the analysis of spatial genetic structure

Considerations of colonization history of an oak species across multiple populations would provide insight into whether different population histories generate near random or significant fine-scale spatial genetic structure. This study used multilocus allozyme genotypes mapped from three populations of Quercus dentata in South Korea: one population, in Mt. Sobaek (SOB), is considered to be recently established from “off-site” seed sources; the second population, located in Dongraedo (DON), Jollanamdo Province may have been established from “on-site” old individuals; and the last population, in Haegumgang (HAE), Gyeongsangnamdo Province, is probably in an intermediate stage between SOB and DON. Coancestry measures (fij), Ripley’s L-statistics, and Wright’s F statistics were calculated to examine the distribution of individuals and spatial genetic structure both within and between populations. Ripley’s L-statistics indicated significant aggregation of individuals, and patterns varied depending on populations. A significant positive fine-scale genetic structure at 10 m distance was detected in population DON, whereas SOB and HAE populations mostly showed very weak patterns and indeed genotypes were essentially randomly distributed. These results appear to be consistent with the proposed histories of population establishment. The levels of genetic diversity within populations of Q. dentata examined in this study (He=0.103) were lower than in most of the oaks, which may reflect rarity and discontinuity in the distribution of Q. dentata. A small but significant deficit of heterozygosity was detected within populations (pooled FIS=0.040), which is also consistent with most of the examined oaks. Low but significant differentiation between the three populations of Q. dentata (mean FST=0.030) agrees with that found for other oaks in South Korea, reflecting long-distance pollen movement by wind.