Strong Spatial Genetic Structure Research Articles

Environmental selection and gene flow jointly determine the population genetic diversity and structure of Diaphanosoma dubium along a watershed elevation

Biodiversity of local communities has been found to generally decrease with elevation. However, the elevational patterns of intraspecific genetic diversity remain unclear, especially in passive dispersers and species with short life histories. In this study, we investigated the populations of a tropical dominant Cladoceran, Diaphanosoma dubium, along elevation in the largest watershed of South China. The studied populations were grouped into four regional groups based on elevation and habitat connectivity. No significant elevation pattern was observed for mitochondrial genetic diversity, but nuclear diversity was influenced by habitat type. The haplotype network showed a radial pattern with a common haplotype at the centre, and many private haplotypes existed in each regional group. Four clusters of D. dubium populations were identified and exactly corresponding to the four investigated regions, indicating a strong spatial genetic structure. Weak but significant isolation by distance (IBD) supported the critical role of environmental selection with elevation. Precipitation significantly explained population genetic variation at the watershed scale. Bidirectional gene flow was a common pattern that occurred among the four regional groups. Our results highlight that habitat selection with gene flow plays an important role in shaping the genetic pattern of tropical freshwater Cladocera along an elevational gradient.

Genetic structure shows the presence of small-scale management units in a relict tree species.

Identifying conservation units is crucial for the effective conservation of threatened species. Previous cases are almost exclusively based on large-scale but coarse sampling for genetic structure analyses. Significant genetic structure can occur within a small range, and thus multiple conservation units may exist in narrowly distributed plants. However, small-scale genetic structure is often overlooked in conservation planning especially for wind-pollinated and wind-dispersed trees, largely due to the absence of dense and elaborate sampling. In this study, we focused on a representative endangered relict plant, Metasequoia glyptostroboides. Using both nuclear microsatellites (nSSRs) and chloroplast DNA (cpDNA) fragments, we sampled across the narrow distribution range of this species and determined its conservation units by exploring its genetic structure and historical demography. cpDNA haplotypes were classified into two groups, but mixed in space, suggesting that the existent wild trees of M. glyptostroboides cannot be divided into different evolutionarily significant units. However, using nSSRs, we detected strong spatial genetic structure, with significant genetic differentiation and weak gene flow between the samples in the east of the species' distribution range and other samples. The divergence between the two nSSR groups was dated to the Last Glacial Maximum (c. 19.6 kya), suggesting that such spatial genetic structure has been maintained for a long term. Therefore, these two nSSR groups should be considered as different conservation units, that is, management units, to protect intergroup genetic variations, which is likely to be the outputs of local adaptation. Our findings highlight the necessity to reveal small-scale genetic structure and population demography to improve the conservation strategies of evolutionary potential of endangered plants.

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.

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.

Deforestation is the turning point for the spreading of a weedy epiphyte: an IBM approach

The rapid spread of many weeds into intensely disturbed landscapes is boosted by clonal growth and self-fertilization strategies, which conversely increases the genetic structure of populations. Here, we use empirical and modeling approaches to evaluate the spreading dynamics of Tillandsia recurvata (L.) L. populations, a common epiphytic weed with self-reproduction and clonal growth widespread in dry forests and deforested landscapes in the American continent. We introduce the TRec model, an individual-based approach to simulate the spreading of T. recurvata over time and across landscapes subjected to abrupt changes in tree density with the parameters adjusted according to the empirical genetic data based on microsatellites genotypes. Simulations with this model showed that the strong spatial genetic structure observed from empirical data in T. recurvata can be explained by a rapid increase in abundance and gene flow followed by stabilization after ca. 25 years. TRec model’s results also indicate that deforestation is a turning point for the rapid increase in both individual abundance and gene flow among T. recurvata subpopulations occurring in formerly dense forests. Active reforestation can, in turn, reverse such a scenario, although with a milder intensity. The genetic-based study suggests that anthropogenic changes in landscapes may strongly affect the population dynamics of species with ‘weedy’ traits.

Genetic variation and population structure of clonal Zingiber zerumbet at a fine geographic scale: a comparison with two closely related selfing and outcrossing Zingiber species

BackgroundThere has always been controversy over whether clonal plants have lower genetic diversity than plants that reproduce sexually. These conflicts could be attributed to the fact that few studies have taken into account the mating system of sexually reproducing plants and their phylogenetic distance. Moreover, most clonal plants in these previous studies regularly produce sexual progeny. Here, we describe a study examining the levels of genetic diversity and differentiation within and between local populations of fully clonal Zingiber zerumbet at a microgeographical scale and compare the results with data for the closely related selfing Z. corallinum and outcrossing Z. nudicarpum. Such studies could disentangle the phylogenetic and sexually reproducing effect on genetic variation of clonal plants, and thus contribute to an improved understanding in the clonally reproducing effects on genetic diversity and population structure.ResultsThe results revealed that the level of local population genetic diversity of clonal Z. zerumbet was comparable to that of outcrossing Z. nudicarpum and significantly higher than that of selfing Z. corallinum. However, the level of microgeographic genetic diversity of clonal Z. zerumbet is comparable to that of selfing Z. corallinum and even slightly higher than that of outcrossing Z. nudicarpum. The genetic differentiation among local populations of clonal Z. zerumbet was significantly lower than that of selfing Z. corallinum, but higher than that of outcrossing Z. nudicarpum. A stronger spatial genetic structure appeared within local populations of Z. zerumbet compared with selfing Z. corallinum and outcrossing Z. nudicarpum.ConclusionsOur study shows that fully clonal plants are able not only to maintain a high level of within-population genetic diversity like outcrossing plants, but can also maintain a high level of microgeographic genetic diversity like selfing plant species, probably due to the accumulation of somatic mutations and absence of a capacity for sexual reproduction. We suggest that conservation strategies for the genetic diversity of clonal and selfing plant species should be focused on the protection of all habitat types, especially fragments within ecosystems, while maintenance of large populations is a key to enhance the genetic diversity of outcrossing species.

Genetic variation and genetic structure within metapopulations of two closely related selfing and outcrossing Zingiber species (Zingiberaceae).

Habitat fragmentation strongly affects the genetic diversity of plant populations, and this has always attracted much research interest. Although numerous studies have investigated the effects of habitat fragmentation on the genetic diversity of plant populations, fewer studies have compared species with contrasting breeding systems while accounting for phylogenetic distance. Here, we compare the levels of genetic diversity and differentiation within and among subpopulations in metapopulations (at fine-scale level) of two closely related Zingiber species, selfing Zingiber corallinum and outcrossing Zingiber nudicarpum. Comparisons of the genetic structure of species from unrelated taxa may be confounded by the effects of correlated ecological traits or/and phylogeny. Thus, we possibly reveal the differences in genetic diversity and spatial distribution of genetic variation within metapopulations that relate to mating systems. Compared to outcrossing Z. nudicarpum, the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity was not different. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum, depending on whether the degree of subpopulation isolation surpasses the dispersal ability of pollen and seed. A stronger spatial genetic structure appeared within subpopulations of selfing Z. corallinum potentially due to restricted pollen flow and seed dispersal. In contrast, a weaker genetic structure was apparent in subpopulations of outcrossing Z. nudicarpum most likely caused by extensive pollen movement. Our study shows that high genetic variation can be maintained within metapopulations of selfing Zingiber species, due to increased genetic differentiation intensified primarily by the stochastic force of genetic drift among subpopulations. Therefore, maintenance of natural variability among subpopulations in fragmented areas is key to conserve the full range of genetic diversity of selfing Zingiber species. For outcrossing Zingiber species, maintenance of large populations is an important factor to enhance genetic diversity.Compared to outcrossing Z. nudicarpum, the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity did not differ. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum, depending on whether the degree of subpopulation isolation surpasses the dispersal ability of pollen and seed. Our study shows that selfing Z. corallinum could maintain high genetic diversity through differentiation intensified primarily by the stochastic force of genetic drift among subpopulations at fine-scale level, but not local adaptation.

High genetic diversity and low future habitat suitability: will Cupressus atlantica, endemic to the High Atlas, survive under climate change?

Cupressus atlantica is a narrow endemic species of semi-arid and sub-humid habitats in the western High Atlas, Morocco. We explored the possible dynamics of the species’ range under climatic changes using species distribution modelling (SDM) to identify populations vulnerable to range changes. Additionally, we investigated the spatial genetic structure (SGS), the effective population size and genetic connectivity in natural populations, which may provide important data on demo-genetic processes and support the conservation management of this critically endangered species. The SDM results showed that the current species range constitutes only 49% of the potential distribution. Under the most pessimistic scenarios (RCP6.0 and RCP8.5), a significant reduction in the species range was predicted. However, the projection based on RPC4.5 revealed possible extensions of the habitats suitable for C. atlantica. Potentially, these areas could serve as new habitats that could be used with the assisted migration approach aiming to mitigate the current fragmentation. In terms of the SGS, significant and positive aggregation of relatives was detected up to ca. 100 m. In comparison to other fragmented and endemic species, the detected SGS was weak (Sp = 0.0112). The estimated level of recent gene flow was considerable, which likely prevented a strong SGS and allowed diversity to accumulate (HE = 0.894). The most alarming results concern the effective population size, which was very low in the studied populations (< 53), suggesting a possible increase in inbreeding and loss of diversity in the near future. More effective conservation actions integrating in situ and ex situ measures should be undertaken to prevent extirpation of the species.

Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

Global gene flow releases invasive plants from environmental constraints on genetic diversity

When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area.

Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae).

BackgroundNeotricula aperta is the snail-intermediate host of the parasitic blood-fluke Schistosoma mekongi which causes Mekong schistosomiasis in Cambodia and the Lao PDR. Despite numerous phylogenetic studies only one DNA-sequence based population-genetic study of N. aperta had been published, and the origin, structure and persistence of N. aperta were poorly understood. Consequently, a phylogenetic and population genetic study was performed, with addition of new data to pre-existing DNA-sequences for N. aperta from remote and inaccessible habitats, including one new taxon from Laos and 505 bp of additional DNA-sequence for all sampled taxa,.Principal findingsSpatial Principal Component Analysis revealed the presence of significant spatial-genetic clustering. Genetic-distance-based clustering indicated four populations with near perfect match to a priori defined ecogeographical regions. Spring-dwelling taxa were found to form an ecological isolate relative to other N. aperta. The poor dispersal capabilities suggested by spatial-genetic analyses were confirmed by Bayesian inference of migration rates. Population divergence time estimation implied a mid-Miocene colonisation of the present range, with immediate and rapid radiation in each ecogeographical region. Estimated effective population sizes were large (120–310 thousand).ConclusionsThe strong spatial-genetic structure confirmed the poor dispersal capabilities of N. aperta—suggesting human-mediated reintroduction of disease to controlled areas as the primary reason for control failure. The isolation of the spring-dwelling taxa and ecogeographical structure suggests adaptation of sub-populations to different habitats; the epidemiological significance of this needs investigation. The large effective population sizes indicate that the high population densities observed in surveyed habitats are also present in inaccessible areas; affording great potential for recrudescence driven by animal-reservoir transmission in remote streams. Mid-Miocene colonisation implies heterochronous evolution of these snails and associated schistosomes and suggests against coevolution of snail and parasite. Heterochronicity favours ecological factors as shapers of host-parasite specificity and greater potential for escape from schistosomiasis control through host-switching.

Diversidad y estructura genética de cuatro especies arbóreas clave del Bosque Seco Tropical en Colombia

El Bosque Seco Tropical (bs-T) es uno de los ecosistemas más degradados de Colombia requiriendo acciones urgentes para la conservación de sus relictos remanentes y la restauración de áreas degradadas. La diversidad genética es una herramienta fundamental para identificar áreas prioritarias de conservación in situ, y evaluar la calidad de las poblaciones como fuentes de semilla para su uso en la restauración. Aquí se presentan los resultados de una caracterización genética realizada con marcadores moleculares ISSRs (Inter Simple Sequence Repeats) en 251 individuos de cuatro especies clave del bs-T Colombiano: Bursera simaruba, Platymiscium pinnatum, Hura crepitans y Caesalpinia ebano. Las poblaciones más diversas para las cuatro especies se encontraron en la región del Caribe y en el enclave del Cañón del Chicamocha. Platymiscium pinnatum y B. simaruba también mostraron valores altos de diversidad en el valle del río Cauca y el desierto de La Tatacoa, respectivamente. Además, se evidenció estructura genética en las cuatro especies que podría estar asociada a las transformaciones históricas del bs-T en los periodos geológicos del Pleistoceno y el Holoceno. Finalmente, se identificaron fuentes de semilla en cada región para cada especie y entre ellos se destacan el norte Caribe y el área del enclave del Cañón del Chicamocha, por su riqueza y particularidad genética.

Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a neotropical palm

Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador. This approach allowed us to quantify the separate contributions of each of these two dispersal processes to genetic variation. Compared to continuous forest, fragments had stronger spatial genetic structure, especially among female gametes, and reduced effective population sizes. We found that within and among fragments, allelic diversity was lower and genetic structure higher for female gametes than for male gametes. Moreover, female gametic allelic diversity in fragments decreased with decreasing surrounding forest cover, while male gametic allelic diversity did not. These results indicate that limited seed dispersal within and among fragments restricts genetic diversity and strengthens genetic structure in this system. Although pollen movement may also be impacted by habitat loss and fragmentation, it nonetheless serves to promote gene flow and diversity within and among fragments. Pollen and seed dispersal play distinctive roles in determining patterns of genetic variation in fragmented landscapes, and maintaining the integrity of both dispersal processes will be critical to managing and conserving genetic variation in the face of continuing habitat loss and fragmentation in tropical landscapes.

Population declines, genetic bottlenecks and potential hybridization in sea snakes on Australia's Timor Sea reefs

Population bottlenecks can result in loss of genetic variation, increased extinction risk, and hybridization with related sympatric species. Many challenges are associated with empirical detection of population declines, thus conservation biologists often use molecular approaches as surrogates. This study explored whether declines in abundances of viviparous sea snakes on Australia's Timor Sea reefs could have been foreshadowed using genetic surveys. Ashmore Reef (the largest Timor Sea reef) once hosted large breeding populations of sea snakes. Abundances have declined precipitously since 1994 and Ashmore Reef has been devoid of snakes since 2012. Moreover, high rates of hybridization between two sympatric species have been documented on Timor Sea reefs, possibly associated with sea snake declines. I analysed mitochondrial DNA and 11 nuclear microsatellites for >250 sea snakes from three species, Aipysurus laevis, Aipysurus fuscus and Emdocephalus annulatus, sampled on four Timor Sea reefs in 2002 and 2010. While there was strong spatial genetic structure among reefs, there was little temporal genetic divergence for A. laevis at Ashmore Reef, despite the massive declines in abundance during that temporal window. Positive Tajima's D and Fu's FS values at Ashmore Reef indicated demographic contraction for: A. laevis in 2002 and 2010; E. annulatus (2002); but not A. fuscus (2002). Microsatellites showed inbreeding depression (positive Fis values) and non-random mating (heterozygote deficit) for all three species at Ashmore Reef, consistent with population declines. Bottleneck tests were equivocal, with significant heterozygous excesses at Ashmore Reef, but non-significant M-ratios or mode-shifts in allele frequencies, with the significance of tests differing markedly with microsatellite mutation models. Thus genetic analyses alone would not have been sufficient to provide managers with unequivocal evidence of population declines. There was little evidence for hybridization between A. laevis and A. fuscus, despite previous research suggesting that the Endangered A. fuscus was at risk of reverse speciation secondary to the highly porous reproductive barriers between these species.

Lack of spatial structure for phenotypic and genetic variation despite high self-fertilization in Aquilegia canadensis (Ranunculaceae).

By reducing genetically effective population size and gene flow, self-fertilization should lead to strong spatial genetic structure (SGS). Although the short-lived plant Aquilegia canadensis produces large, complex, nectar-rich flowers, 75% of seed, on average, are self-fertilized. Previous experimental results are consistent with the fine-scale SGS expected in selfing populations. In contrast, key floral traits show no evidence of SGS, despite a significant genetic basis to phenotypic variation within populations. In this study, we attempt to resolve these contradictory results by hierarchically sampling plants from two plots nested within each of seven rock outcrops distributed over several km, and comparing the spatial pattern of phenotypic variation in four floral traits with neutral genetic variation at 10 microsatellite loci. For both floral and microsatellite variation, we detected only weak hierarchical structuring and no isolation by distance. The spatial pattern of variation in floral traits was on par with microsatellite polymorphisms. These results suggest regular long-distance gene flow via pollen. At much finer spatial scales within plots, estimates of relatedness were higher (albeit very low) between nearest neighbors than random plants, and declined with increasing distance between neighbors, which is consistent with highly localized seed dispersal. High selfing should yield SGS, but strong inbreeding depression in A. canadensis likely erodes SGS so that reproductive plants exhibit weak structure typical of outcrossers, especially given that outcrossing and consequent gene flow in this species are mediated by strong-flying hummingbirds and bumble bees.

Naturally fragmented and isolated distribution in subtropical grassland patches affects genetic diversity and structure at different spatial scales: The case of Tibouchina hatschbachii, an endemic shrub from Brazil.

The genetic structure of organisms results from the interactions between life history traits and the ecological and demographic characteristics of the landscape that shape the intra- and interpopulation genetic variation in space and time. In this study, we used a species restricted to islands of grassland vegetation in southern Brazil to investigate the effects of its naturally fragmented distribution on diversity and genetic structure patterns. Diversity and intra- and interpopulational genetic structure were analyzed using polymorphisms of eight nuclear microsatellite markers in 205 individuals of T. hatschbachii and Bayesian and multivariate methods. At the intrapopulation level, populations presented low genetic diversity and strong spatial genetic structure, indicating a greater spatial autocorrelation until ∼50-500 m. At the interpopulation level, genetic variation partitioned into two geographically structured genetic clusters. Gene flow through pollen was more efficient than gene flow by seeds. Genetic structure was influenced locally by seed and pollen dispersal dynamics and regionally by fragmentation of the grassland landscape. This study highlights the importance of geological barriers, and potentially a role for genetic drift, in influencing diversification of species in subtropical grasslands of southern Brazil.

Extensive sib-mating in a refugial population of beech (Fagus sylvatica) growing along a lowland river

Abstract Many temperate and boreal tree species have small and scattered populations near the low-latitude margins of their range that have persisted over extended periods of time in microrefugia. It remains poorly understood how patterns of mating and gene flow influence key components for their long-term persistence such as effective population size or genetic diversity. Yet such information is critical for designing effective protection measures and informing programs for the conservation of forest genetic resources. Here we investigate the mating system and pollen dispersal of a long-term refugial population of beech (Fagus sylvatica), a major European forest tree. This population stretches over ca. 7 km along the ravines of a small lowland river in SW France. We exhaustively mapped the adult population (n = 932 trees) and collected seed families (n = 450 seeds) from 30 mother trees spread across the stand. All individuals were genotyped at 113 SNP markers and submitted to paternity analyses. We estimated various mating parameters and tested whether among-individual variation was related with the ecological neighbourhood of the mother tree. A unique father could be identified for all seeds analysed. We detected neither pollen immigration nor selfing events. Instead, we observed extensive mating between neighbouring trees that resulted in a very steep decline of the pollen dispersal kernel and a low effective number of fathers (median Nep = 7.9). In turn, male fecundity was tightly related with the distance between mates. The adult population showed an exceptionally strong and far-reaching spatial genetic structure indicating that neighbouring trees are most often sibs. The predominant mating between these neighbours suggests that patterns of reproduction and pollen flow are not constrained by cross-compatibility issues. Instead, dense conspecific neighbourhoods even tend to bar long-distance pollen flow by saturating the stigmas of mother trees through pollen swamping. The observed patterns are a direct consequence of the refugial habitat that imposes the population’s linear distribution and whose dense vegetation represents a further obstacle to pollen dispersal. The elevated capacity of sib-mating might be a microevolutionary consequence of the population’s long-term persistence in isolation. The resulting spatial genetic structure and the critical role of tree density in assuring an effective reproduction have important consequences for the design of forest genetic resources programs as well as for the conservation management of refugial and other riparian tree populations.

A fig tree in a concrete jungle: fine-scale population genetic structure of the cluster fig Ficus racemosa in an urban environment

Urban vegetation is an essential requirement in cities for mitigating pollution, heat island effects and providing food and shelter to urban fauna. Efforts to conserve and augment green cover in cities, however, often lack data on the genetic diversity of urban trees, which could be crucial to the success of such programmes. We investigate the population genetics of the cluster fig Ficus racemosa, which occurs naturally in Indian cities and is a keystone species for urban fauna. Genetic analysis of 51 F. racemosa trees in urban Bangalore, India, shows no evidence of inbreeding; the overall inbreeding coefficient (F is ) across 12 microsatellite markers (0.0366) was non-significant with no evidence of heterozygote deficit. Spatial genetic structure (SGS) analysis of 47 trees showed an overall negative relationship between kinship coefficient and spatial distance, with strong SGS at distances <1 km. The absence of heterozygote deficit is likely due to the fig’s obligate mutualistic association with fig wasps which pollinate their flowers even across long distances. However, the strong SGS at short distances could result from clumped seed dispersal close to natal trees. Therefore, the pattern of population genetics for F. racemosa from urban Bangalore likely results from short-distance seed dispersal and long-distance pollen flow. Despite the scattered and fragmented nature of green areas within cities, these gene mobility factors maintain robust population genetics in F. racemosa even at low population densities. The same may not apply for Ficus species that are planted as vegetative cuttings in cities and therefore may have limited genetic diversity.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits.