Fine-scale Spatial Genetic Structure Research Articles

Genetic diversity, clonal diversity and fine-scale spatial genetic structure of the white and red fruit color morphs of Fragaria pentaphylla populations

Genetic diversity, clonal diversity and fine-scale spatial genetic structure of the white and red fruit color morphs of Fragaria pentaphylla populations

Fine-scale spatial genetic structure and dispersal among Italian smooth newt populations in a rural landscape

Amphibians are particularly sensitive to habitat loss and fragmentation caused by the intensification and modernization of farming occurring in the second half of the twentieth century in the Mediterranean basin. However, artificial water bodies, associated with traditional husbandry, proved to be important surrogate for amphibian feeding and reproduction. Here, multilocus genotypes were used to investigate the spatial population structure of Lissotriton vulgaris meridionalis and the role of drinking troughs in supporting viable breeding populations within a rural landscape interested by traditional husbandry and agriculture. Our genetic analysis highlighted the conservation value and the potential stepping-stone function of artificial aquatic sites in the dispersal of the species and for the gene flow maintenance. Indeed, populations of drinking troughs show allelic richness and heterozygosity levels comparable to those from natural ponds and there is no great evidence of genetic bottlenecks. A complex system of artificial aquatic sites and few natural wetlands was identified sustaining a well-structured network of demes highly interconnected with themselves and natural aquatic sites. The conservation of the identified genetic clusters may be useful to prevent further population declines and future loss of genetic diversity within the study area characterized by scarce natural wetlands that frequently dried because of agricultural practices and strong seasonality. Site-specific protection measures are needed to contrast the progressive disappearance of drinking troughs observed in the last years in Italy because of the abandonment of traditional farming practices in favour of modern agriculture and intensive farming.

Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania

Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.

Correction: Genetic diversity and fine-scale spatial genetic structure of unmanaged old-growth versus managed second-growth populations of Scots pine (Pinus sylvestris L.) in Lithuania

Correction: Genetic diversity and fine-scale spatial genetic structure of unmanaged old-growth versus managed second-growth populations of Scots pine (Pinus sylvestris L.) in Lithuania

Do habitat fragmentation and degradation influence the strength of fine-scale spatial genetic structure in plants? A global meta-analysis.

As primarily sessile organisms, plants often show a non-random spatial distribution of genotypes over distance. This process known as fine-scale spatial genetic structure (FSGS) has been suggested through systematic reviews to depend on life form, mating system, and pollen and seed dispersal vectors, while there is no consensus on its behaviour due to external factors, such as anthropogenic habitat changes. By conducting a systematic review and global meta-analysis of empirical FSGS studies, we aimed to evaluate how anthropogenic habitat fragmentation and degradation influence the strength of FSGS in plant populations by means of the Sp statistic. Moreover, we tested how pollination and seed dispersal vectors contribute to the variation of the Sp statistic. We retrieved 243 FSGS studies from 1960 to 2020 of which only 65 were informative for the systematic review. Most empirical studies comprised outcrossers (84%) and trees (67%), with few herbs (23%) and scarce annual species (2%). In weighted meta-analyses for 116 plant populations (31 studies), we did not detect significant effects in the magnitude of effect sizes for the Sp statistic among undisturbed, degraded and fragmented habitats. Results showed significant effects for seed dispersal vectors, but not for pollination. Overall, we observed high variation among the effect sizes (not related to the goodness-of-fit of mixed models) of habitat status, pollination and seed dispersal categories, which precludes identifying biological trends on the Sp statistic. More empirical studies are needed that contrast multiple plant populations in disturbed versus undisturbed habitats, and by increasing the taxonomic groups, such as herbs and annual plants.

Genetic diversity and fine-scale spatial genetic structure of unmanaged old-growth versus managed second-growth populations of Scots pine (Pinus sylvestris L.) in Lithuania

Genetic diversity and fine-scale spatial genetic structure of unmanaged old-growth versus managed second-growth populations of Scots pine (Pinus sylvestris L.) in Lithuania

Fine-Scale Spatial Genetic Structure of Remnant Populations of Abies religiosa, in a Temperate Forest in Central Mexico

Genetic structure of a population can be molded by the resistance of the landscape or the distance between populations that function as barriers to gene flow. We analyzed the population genetic structure of Abies religiosa on a fine spatial scale and examined isolation models by resistance and distance. We collected vegetative tissue from populations located at the altitudinal extremes of the distribution range of the species on three slopes of La Malinche National Park (LMNP) (South, North, and East) in central Mexico. Genomic DNA was obtained using the CTAB 2X method, and eight microsatellite chloroplast loci were amplified. The genetic structure was identified based on an Analysis of Molecular Variance, a Discriminant Analysis of Principal Components with cross-validation and a spatial Principal Component Analysis using the Gabriel-type connectivity network. The isolation hypotheses were evaluated by constructing partial Mantel tests using Reciprocal Causal Modeling and Maximum Likelihood Population Effects models. A genetic structure of isolation by resistance to elevation was identified, and two genetic groups were recognized: one including populations of the South slope and the other comprising populations of the North and East slopes. We detected in Abies religiosa populations of the LMNP an isolation by resistance to elevation that determines the genetic structure, and the greatest genetic exchange between groups of populations located at higher altitudes. It is suggested to promote the connectivity between slopes through assisted migration and immediately halt land-use changes, as part of the actions to preserve genetic diversity in the LMPN. This study contributes to the knowledge of the spatial genetic structure of species at risk in the Mexican temperate forest for their conservation.

Limited seed dispersal shapes fine‐scale spatial genetic structure in a Neotropical dioecious large‐seeded palm

AbstractSeed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine‐scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large‐seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent‐mediated seed dispersal has a stronger influence than insect‐mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large‐seeded plants. Rodent‐mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity.Abstract in Spanish is available with online material.

High outcrossing rates in a self-compatible and highly aggregated host-generalist mistletoe.

Plants have evolved various strategies to avoid inbreeding, but the mass flowering displayed by many plants predisposes them to within-plant pollen movements and self-pollination. Mistletoes often aggregate at multiple spatial scales. Their bird pollinators often visit several flowers of the same individual and of others on the same host tree. We hypothesized that hermaphroditic mistletoes have self-incompatibility mechanisms that reduce or prevent selfing. Whether their spatial distribution, affected by host specificity, host distribution, and the behaviour of seed dispersers, influences their mating system and population genetic structure remains unclear. We studied how mating system and spatial distribution affect genetic structure in four populations of the host-generalist mistletoe Dendrophthoe pentandra in southwestern China using microsatellite markers and progeny arrays. We also characterized the fine-scale spatial genetic structure among 166 mistletoes from four host trees in one population. Prevalence and intensity of infection both appeared to vary among host species, strongly affecting the degree of aggregation. Host tree size had a strong effect on infection intensity. Surprisingly, manual pollination experiments indicated that D. pentandra is self-compatible, but genetic analyses revealed that outcrossing rates were higher than expected in all four populations (MLTR tm 0.83-1.20, Bayesian tm 0.772-0.952). Spatial genetic structure was associated with distance between host trees but not at shorter scales (within hosts). Our results demonstrate that the combination of bird pollination, bird-mediated seed dispersal, and post-dispersal processes result in outcrossing and maintain relatively high diversity in the presence of biparental inbreeding, despite very high local densities and possible self-compatibility.

Genetic diversity and fine-scale spatial genetic structure of the near-threatened Pinus gerardiana in Gardiz, Afghanistan

Background and aims – Chilgoza pine (Pinus gerardiana) is a near-threatened tree species from the north-western Himalayas. This species is the economically most important pine in Afghanistan because of its edible nuts; however, its distribution range is disjunct and restricted to a few isolated regions. The IUCN lists Chilgoza as a near threatened species because of overexploitation of its nuts and a declining population trend. This research is the first in-depth analysis of the genetic variability and structure of Chilgoza in Afghanistan using microsatellite markers. Material and methods –We tested cross-amplification of 44 SSR markers developed for pine species. Eight polymorphic EST-SSRs were genotyped in a natural Chilgoza population in Gardiz, Afghanistan. To evaluate the genetic diversity, fine-scale spatial genetic structure (SGS), signatures of bottleneck events, and the effective population size, 191 trees were sampled and genotyped. Based on the diameter at breast height, individuals were classified as young or old trees. Key results – Genetic variation in the whole population was moderate. For individual markers, He ranged from 0.130 to 0.515 (mean = 0.338) and Ho from 0.118 to 0.542 (mean = 0.328). The expected heterozygosity in young trees was slightly lower than in old trees. The SGS was stronger for young trees (Sp = 0.0100) than for old trees (Sp = 0.0029). Heterozygosity excess analysis detected no recent population size reduction, but the M ratio revealed an ancient and prolonged bottleneck in the Chilgoza population. Conclusion – Identification of suitable EST-SSRs for future studies of natural Chilgoza populations provides important tools for the conservation of the species. Despite the moderate genetic variation in Gardiz, scarcity of natural regeneration is likely to reduce the genetic variation and adaptability in future generations. Our results indicated a slight decrease in genetic diversity and stronger SGS in young trees calling for conservation measures fostering natural regeneration.

Clonal Diversity and Fine-Scale Genetic Structure of a Keystone Species: Ilex aquifolium

Resprouting species, such as English holly (Ilex aquifolium L.), can be severely affected by long-lasting forest management. In the present study, the clonal and fine-scale spatial genetic structure (FSGS) of English holly are evaluated in a sub-Mediterranean mixed forest of Central Spain, where this species was subjected to different and intense human interventions for centuries, including coppicing in dense structures and in open woody pastures. Using seven microsatellite loci, we assessed the contribution of clonal and sexual reproduction to the diversity of holly in both areas and the fine-scale genetic structure was evaluated. For the dense coppiced area, the results showed high clonal diversity derived mainly from stem resprouting. Stems were separated an average of 3 m and up to 10 m, and dense aggregations of stems sometimes included various genotypes. The results also showed recent seed recruitment leading to small unique and isolated genotypes. Furthermore, FSGS was detected at close distances as being stronger in the coppiced area than in the open woody pasture area, especially for individuals of greater diameter at breast height. The results obtained suggest that current management strategies are not negatively affecting the genetic diversity of this species.

Genetic Diversity and Fine-Scale Spatial Genetic Structure of the Endangered Shrub Birch (Betula humilis Schrk.) Populations in Protected and Unprotected Areas

The genetic diversity of natural populations is a key factor in the success of long-term ecosystem protection. We studied the genetic diversity and spatial genetic structure (SGS) in three endangered shrub birch (Betula humilis) populations using seven nuclear microsatellite loci. The highest genetic variation was found in the restored Szuszalewo population in Biebrza National Park, where active prevention of thicket forest succession was recently conducted. The results of bottleneck tests were not statistically significant in each locality, although a genetic indication for population reduction was detected in the Rospuda stand, which is not actively protected. The Bayesian clustering, principal coordinates analysis, and FST estimates revealed the greatest difference between Magdzie Bagno and Rospuda samples. SGS was found in all B. humilis stands; however, it was the strongest in the Rospuda locality, where pollen and seed dispersal was limited by dense clusters of shrub birch ramets scattered among forest and brushwood plants. The weakest SGS, also supported by finding some sibling pairs in distant locations, was observed in the Szuszalewo population. The aforementioned results indicate that the active protection practices may impose an immediate beneficial effect on the restoration and maintenance of the B. humilis populations.

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.

Stand development stages and recruitment patterns influence fine-scale spatial genetic structure in two Patagonian Nothofagus species

Key messageNothofagus alpina (Poepp. et Endl.) Oerst. and Nothofagus obliqua (Mirb.) Oerst forests have strong fine-scale spatial genetic structures. The intensity of genetic structure patterns differed according to species, stand development stages, life stages, and spatial arrangement of regeneration groups. This data becomes useful for forest management as it provides an understanding of how populations evolve as well as of the consequences of disturbances and enables the establishment of sampling strategies.ContextThe understanding of fine-scale spatial genetic structure in natural populations is useful for forest management. Although Nothofagus alpina (Poepp. et Endl.) Oerst. and N. obliqua (Mirb.) are important species of the Patagonian forest, little is known about the genetic structure of their populations.AimsThe main objectives were to investigate the differences in fine-scale spatial genetic structure among mature tree populations of both species considering two stands at different development stages. Genetic structure was also evaluated among life stages and spatial distribution groups of regeneration within the old-growth stand.MethodsGenetic structure was examined by microsatellite DNA analysis of regeneration and mature tree populations of both species (around 1300 individuals). Gene dispersal distance was additionally estimated.ResultsIn both stands and species, strong fine-scale spatial genetic structure and short dispersal distance were found. This pattern was stronger in the early successional forest, in N. obliqua populations, in earlier life stages, and in scattered regeneration.ConclusionStand development stages and recruitment patterns influence the fine-scale spatial genetic structure of both Nothofagus species. However, the genetic structure also differs between species.

Reproductive strategy of a temperate canopy tree Tilia cordata Mill. (Malvaceae) is related to temperature during flowering and density of recent recruits

Facultative clonality is extremely common in plants, but the relative emphasis on sexual versus asexual reproduction varies both between and within species, which in turn may influence individual fitness and population persistence. Tilia cordata is a temperate, entomophilous canopy tree that is partially clonal. Favourably warm climatic conditions have been linked with successful sexual reproduction in the species with clonality being suggested as the reason for population persistence in colder periods. Despite this the extent, character and structure of asexual reproduction in the species have never been described, nor has its relationship with climate. Fine-scale spatial genetic structure was assessed in 23 stands across a latitudinal gradient. The proportion of individuals that are of clonal origin has a wide range with a mean of ~43%. Genetic diversity is high, with even mostly clonal stand possessing several distinct genotypes. A beta regression model shows that historic summer temperatures and density of recent recruits are predictors of the proportion of clonal recruitment. Clonal reproduction is less important in stands that experience higher temperatures during flowering while stands with more saplings have more clones. Additional factors likely affect the balance between the two reproductive modes. The climatic relationship suggests a trend towards a higher proportion of recruitment from seed in a warming climate, although factors such as herbivory may prevent this.

High pollen immigration but no gene flow via-seed into a Genetic Conservation Unit of the endangered Picea omorika after disturbance

Studying how genetic diversity is transmitted between generations is critical for assessing the survival prospects of fragmented forest tree populations. This is especially urgent in the case of rare, endangered species that are at high risk of extinction and/or exceptionally susceptible to climate change, and are thus to be prioritised for conservation initiatives. We performed the first assessment of gene flow patterns by parentage analysis in the IUCN red-listed Serbian spruce [Picea omorika (Panč.) Purk.], within a Genetic Conservation Unit (GCU) which was exposed to fire disturbance 30 years ago. Parentage analysis was based on assigning the parentage of 104 juveniles to all the adult trees (48) present in the 2.8 ha population. All individuals were genotyped at 11 highly informative nuclear microsatellite markers.We found that fire disturbance triggered natural regeneration, usually poor to absent in Serbian spruce, and boosted pollen immigration (66%), which is reported as rather modest among undisturbed populations of this species. Seed immigration was absent, coherently with what was previously hypothesised for natural, undisturbed populations. Thus, the immigration of new gametes into the studied Serbian spruce population was accomplished exclusively through pollen gene flow, at a rate sufficient to counteract, at least in the short term, genetic drift. Furthermore, the abundant post-disturbance pollen immigration most likely accounts for the lack of fine-scale spatial genetic structure (SGS) in the juvenile cohort, contrary to the SGS observed in the adult cohort which is amongst the strongest ever recorded in anemophilous forest tree species. Finally, as generally found in forest trees, individual reproductive success was uneven among individuals, with 25% of local adults siring 70% of the sampled juveniles.Our results on post-disturbance gene flow patterns in the only Serbian spruce population with reportedly abundant regeneration complement the outcomes of previous genetic studies while providing essential information for the dynamic management and conservation of this rare and endangered species severely threatened by climate warming. Tracking the temporal development of gene flow parameters and the consequences of gene flow on genetic diversity are two cornerstones of future forest genetic monitoring programs, which are particularly important for GCUs. In particular, monitoring the genetic diversity of forest regeneration is deemed as the key for understanding changes that otherwise would remain mostly untraceable in long-lived organisms such as forest trees.

Genetic Diversity and Fine-Scale Spatial Genetic Structure of Unmanaged Old-Growth Versus Managed Second-Growth Populations of Scots Pine (Pinus Sylvestris L.) in Lithuania: Effects of Systematic Tending

Genetic Diversity and Fine-Scale Spatial Genetic Structure of Unmanaged Old-Growth Versus Managed Second-Growth Populations of Scots Pine (Pinus Sylvestris L.) in Lithuania: Effects of Systematic Tending

There Is No 'Rule of Thumb': Genomic Filter Settings for a Small Plant Population to Obtain Unbiased Gene Flow Estimates.

The application of high-density polymorphic single-nucleotide polymorphisms (SNP) markers derived from high-throughput sequencing methods has heralded plenty of biological questions about the linkages of processes operating at micro- and macroevolutionary scales. However, the effects of SNP filtering practices on population genetic inference have received much less attention. By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure – SGS) gene flow estimates. We focus specifically on these manifestations in small plant populations, and particularly, in the rare tropical plant species Dinizia jueirana-facao, where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05–0.35) and MD (0–20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σrt = 41.8 m) was ∼ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao, which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no ‘rule of thumb’ for bioinformatic filtering and that relying on default program settings is not advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates.

Barrier to Gene Flow of Grey Mangrove Avicennia marina Populations in the Malay Peninsula as Revealed From Nuclear Microsatellites and Chloroplast Haplotypes

Contemporary mangrove forest areas took shape historically and their genetic connectivity depends on sea-faring propagules, subsequent settlement, and persistence in suitable environments. Mangrove species world-wide may experience genetic breaks caused by major land barriers or opposing ocean currents influencing their population genetic structure. For Malay Peninsula, several aquatic species showed strong genetic differentiation between East and West coast regions due to the Sunda shelf flooding since the Last Glacial Maximum. In this study genetic diversity and structure of Avicennia marina populations in Malay Peninsula were assessed using nuclear microsatellite markers and chloroplast sequences. Even though all populations showed identical morphological features of A. marina, three evolutionary significant units were obtained with nuclear and cytoplasmic markers. Avicennia marina along a 586 km stretch of the West coast differed strongly from populations along an 80 km stretch of the East coast featuring chloroplast capture of Avicennia alba in an introgressive A. marina. Over and above this expected East-West division, an intra-regional subdivision was detected among A. marina populations in the narrowest region of the Strait of Malacca. The latter genetic break was supported by an amova, structure, and barrier analysis whereas RST > FST indicated an evolutionary signal of long-lasting divergence. Two different haplotypes along the Western coast showed phylogeographic relationship with either a northern or a putative southern lineage, thereby assuming two Avicennia sources facing each other during Holocene occupation with prolonged separation in the Strait of Malacca. Migrate-n model testing supported a northward unidirectional stepping-stone migration route, although with an unclear directionality at the genetic break position, most likely due to weak oceanic currents. Low levels of genetic diversity and southward connectivity was detected for East coast Avicennia populations. We compared the fine-scale spatial genetic structure (FSGS) of Avicennia populations along the exposed coast in the East vs. the sheltered coast in the West. A majority of transects from both coastlines revealed no within-site kinship-based FSGS, although the remoteness of the open sea is important for Avicennia patches to maintain a neighborhood. The results provide new insights for mangrove researchers and managers for future in-depth ecological-genetic-based species conservation efforts in Malay Peninsula.

Fine‐scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (F CT = 0.148) was an order of magnitude greater than between elevations within sites (F SC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.