Genetic structure of age classes in Camellia japonica (Theaceae)

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.

Complete nucleotide sequence of chrysanthemum mosaic-associated virus, a novel emaravirus infecting chrysanthemum

Here, we report the complete genome sequence of chrysanthemum mosaic-associated virus (ChMaV), a putative new member of the genus Emaravirus. The ChMaV genome comprises seven negative-sense RNA segments (RNAs 1, 2, 3a, 3b, 4, 5, and 6), and the amino acid sequences of its RNA-dependent RNA polymerase (RNA1), glycoprotein precursor (RNA2), nucleocapsid protein (RNA3), and movement protein (RNA4) showed the closest relationship to pear chlorotic leaf spot-associated virus. Phylogenetic analysis showed that it clusters with emaraviruses whose host plants originate from East Asia.

A complex virome including two distinct emaraviruses associated with virus-like symptoms in Camellia japonica

Camellia japonica plants manifesting a complex and variable spectrum of viral symptoms like chlorotic ringspots, necrotic rings, yellowing with necrotic rings, yellow mottle, leaves and petals deformations, and flower color-breaking have been studied since 1940, mainly by electron microscopic analyses; however, a strong correlation between the symptoms and one or more well-characterized viruses was never verified. In this work, samples collected from symptomatic plants were analyzed using the next-generation sequencing technique, and a complex virome composed of members of the Betaflexiviridae and Fimoviridae families was identified. In particular, the genomic fragments typical of the emaravirus group were organized in the genomes of two new emaraviruses species, tentatively named Camellia japonica-associated emaravirus 1 and 2. They are the first emaraviruses described in camellia plants and found in symptomatic plants. At the same time, in both symptomatic and asymptomatic plants, five betaflexivirus isolates were detected that, based on amino acid sequence comparisons, can be considered two new isolates of the recently characterized camellia ringspot-associated virus 1 and 2 (CRSaV-1/2). These recently identified betaflexiviruses associated with C. japonica disease show an unusual hyper-conservation of the coat protein at the amino acid level. The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are MN385581, MN532567, MN532565, MN385582, MN532566, MN385573, MN385577, MN385574, MN385578, MN385575, MN385579, MN385576, MN385580, MN557024, MN557025, MN557026, MN557027, and MN557028.

Janzen-Connell effects shape gene flow patterns and realized fitness in the tropical dioecious tree Spondias purpurea (ANACARDIACEAE)

Pollination and seed dispersal patterns determine gene flow within plant populations. In tropical forests, a high proportion of trees are dioecious, insect pollinated and dispersed by vertebrates. Dispersal vectors and density dependent factors may modulate realized gene flow and influence the magnitude of Fine Scale Genetic Structure (FSGS), affecting individual fitness. Spondias purpurea is a vertebrate-dispersed, insect-pollinated dioecious tropical tree. We assessed the influence of sex ratio, effective and realized gene flow on genetic diversity, FSGS and individual fitness within a 30 ha plot in the tropical dry forest reserve of Chamela-Cuixmala, Mexico. All individuals within the plot were tagged, geo-referenced and sampled for genetic analysis. We measured dbh and monitored sex expression during two reproductive seasons for all individuals. We collected seeds directly from maternal trees for effective pollen dispersal analysis, and analyzed established seedlings to assess realized pollen and seed dispersal. Nine microsatellite loci were used to describe genetic diversity parameters, FSGS and gene flow patterns among different size classes. A total of 354 individuals were located and classified into three size classes based on their dbh (<10, 10–20, and >20 cm). Population sex ratios were male biased and diametric size distributions differed among sexes, these differences may be the result of precocious male reproduction at early stages. Autocorrelation analyses indicate low FSGS (Fj <0.07) across all size classes. Long realized pollen and seed dispersal and differences among effective and realized gene flow were detected. In our study site low FSGS is associated with high gene flow levels. Effective and realized gene flow indicate a population recruitment curve indicating Janzen-Connell effects and suggesting fitness advantages for long-distance pollen and seed dispersal events.

North American Douglas-fir (P. menziesii) in Europe: establishment and reproduction within new geographic space without consequences for its genetic diversity

Genetic admixture and plasticity along with propagule pressure, large seed dispersal distances and fast adaptation support successful establishment and spread of introduced species outside their native range. Consequently, introductions may display climatic niche shifts in the introduced range. Douglas-fir, a controversial forest and ornamental conifer represented by two ecologically different and hybridising varieties, was transferred multiple times outside the native range in North America. Here, we compare climatic and genetic patterns of 38 native populations from North America with six old Pseudotsuga menziesii populations with natural regeneration in the introduced range in Central Europe. Following variety and geographic origin assessment of introduced populations, genotypic and climatic data were examined for signatures of inter-varietal gene flow, reduced genetic diversity, presence of fine-scale spatial genetic structure (SGS), dispersal patterns, and climate similarities between native and introduced range. In the introduced range, dominating coastal variety originated from a restricted area in the US, whereas the interior variety, with limited presence in the European sites, displayed wider geographic origin. Variety hybrids with contributing coastal, but not the interior parent were identified. Differences in genetic diversity between both ranges, but also among the parent and their respective offspring populations in Europe were not found. Old populations in general lacked any SGS, whereas natural regeneration revealed different patterns of SGS. Distances of propagule dispersal ranged between 2.5 and 92 m. The climate of the studied European introduced range was most similar to the climate of the coastal variety from the western Cascade range from which the majority of the analysed coastal European Douglas-fir, but not the European interior variety, was assigned to originate. The results we present here shed not only light on dynamics of invasive species in the introduced range in general, but also allow for refinement of climatic niche modeling when using lower than species level.

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.

Genetic Diversity among Age Classes of a Pinus sylvestris (L.) Population from the Białowieża Primeval Forest, Poland

The Białowieża Primeval Forest (BPF) is Europe’s last primeval forest and an irreplaceable area for biodiversity conservation due to its size, protection status, and substantially undisturbed nature. There is no other forest in Europe with such a large surface representing highly-advanced natural succession. This article reports on the first analysis of the genetic variability and demographic structure of a self-renewed Pinus sylvestris population located in BPF, using both chloroplast and mitochondrial DNA markers. The analysis of molecular variance (AMOVA) for chloroplast simple sequence repeats (cpSSRs) revealed a significant genetic differentiation among age classes that accounted for about 2% of the total variance, comparable to those reported among different populations of Scots pine. None of the 117 detected chloroplast haplotypes were common to all age classes. Haplotype diversity ranged from 0.370 to 0.415 for cpSSRs and from 0.320 to 0.455 for mitochondrial markers. The genetic variation of the studied age classes—represented by mitochondrial markers—strongly depicts the maternal genetic structure, indicating limited seed dispersal. Temporal genetic substructuring is maintained within a self-renewed population of Scots pine from the BPF.

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

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

Spatial genetic structure ofManilkara maxima(Sapotaceae), a tree species from the Brazilian Atlantic forest

Habitat fragmentation may lead to spatial genetic structuring of plant populations, but the magnitude of this effect differs among species. In this study, the effects of fragmentation on spatial genetic structure ofManilkara maxima, an ecologically important tree species endemic to the Atlantic forest of southern Bahia, Brazil, were examined. To address this issue, 222 individuals were sampled across two large-forest sites (200 and 400 ha) and one site comprising eight small fragments (5, 10 and 25 ha) roughly 35 y old. Five microsatellite loci were used. In general,M. maximaexhibited limited genetic structuring within and across the sites examined. At the landscape scale, genetic structure was not shaped by isolation by distance. Within individual sites, weak to moderate genetic structure was observed for both adults and saplings, which represented pre- and post-fragmentation, respectively. Sapling genetic structure did not clearly vary among the study sites, suggesting fragmentation has not affected spatial genetic structure. High levels of migration were observed, which would help maintain genetic connectivity. Taken together, these results suggestM. maxima, a long-lived tree that naturally occurs in low densities, may have limited spatial genetic structuring both within and across forest patches.

Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana

Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

Spatial and temporal population genetic variation and structure of Nothotsuga longibracteata (Pinaceae), a relic conifer species endemic to subtropical China

Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR) and chloroplast microsatellites (cpSSR). A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.

Is the post-disturbance composition of a plant population determined by selection for outcrossed seedlings or by the composition of the seedbank?

Seedbanks are expected to buffer populations against disturbances, such as fire, that could alter the genetic composition of smaller, ephemeral adult populations. However, seedling genotypes may be influenced by the spatially heterogeneous nature of both the seedbank and the disturbance (for example, germination may vary with local disturbance) and also by selection acting on germination and post-germination performance. We used microsatellite-DNA surveys of seedlings emerging from the soil-stored seedbanks of Grevillea macleayana after wildfire to compare diversity and spatial structure in seedlings and adults, and through resampling of the seedling data set, to determine whether the resultant adult population reflected the effects of selection or random seedling mortality. The large post-fire seedling cohorts captured the full allelic diversity of the pre-fire adult population. However, we found a mismatch in the genotypic structure of adults and seedlings. Seedlings displayed larger heterozygous deficits than adults; however, over the ensuing 11 years, seedling heterozygosity eventually matched values for the pre-fire adults. Increasing heterozygosity among adults has generally been attributed to heterosis and/or reduction in Wahlund effects via self-thinning. Resampling of early post-fire seedlings to generate samples of equivalent size to survivors at 11 years showed that increases in heterozygosity must be driven by selection favouring outcrossed seed. This finding is important in an evolutionary context but also has implications for the restoration of natural or managed populations where a seedbank is a viable source of recruits.

Fine-scale genetic structure of Nothofagus pumilio (lenga) at contrasting elevations of the altitudinal gradient

Montane forests provide the natural framework to test for various ecological settings at distinct elevations as they may affect population demography, which in turn will affect the spatial genetic structure (SGS). We analyzed the fine-scale SGS of Nothofagus pumilio, which dominates mountain areas of Patagonia, in three pairs of sites at contrasting elevations (low- vs. high-elevation). Within a total area of 1 ha fresh leaf tissue from 90 individuals was collected at each of the six studied stands following a spatially explicit sampling design. Population genetic diversity parameters were analyzed for all sampled individuals using five polymorphic isozyme loci, and a subset of 50 individuals per stand were also screened for five microsatellite loci. The SGS was assessed on 50 individuals/stand, using the combined datasets of isozymes and microsatellites. Most low-elevation stands consisted of older individuals with complex age structures and genetically diverse plots. In contrast, high-elevation stands and one post-fire low-elevation population yielded even-aged structures with evidence of growth suppression, and were genetically homogeneous. All stands yielded significant SGS. Similarly to mature stands of the non-sprouter congener Nothofagus dombeyi, multi-age low-altitude N. pumilio yielded significant SGS weakened by competing species of the understory and the formation of seedling banks. Alike the sprouter Nothofagus antarctica, high-altitude stands produced significant SGS as a consequence of occasional seedling establishment reinforced by vegetative spread.

Heterozygote excess through life history stages in Cestrum miradorense Francey (Solanaceae), an endemic shrub in a fragmented cloud forest habitat

Comparisons of genetic diversity and population genetic structure among different life history stages provide important information on the effect of the different forces and micro-evolutionary processes that mould diversity and genetic structure after fragmentation. Here we assessed genetic diversity and population genetic structure using 32 allozymic loci in adults, seeds, seedlings and juveniles of eight populations of the micro-endemic shrub Cestrum miradorense in a highly fragmented cloud forest in central-eastern Mexico. We expected that due to its long history or rarity, this species may have endured the negative effects of fragmentation and would show moderate to high levels of genetic diversity. High genetic diversity (H(e) = 0.445 ± 0.03), heterozygote excess (F(IT) = -0.478 ± 0.034, F(IS) = -0.578 ± 0.023) and low population differentiation (F(ST) = 0.064 ± 0.011) were found. Seeds had higher genetic diversity (H(e) = 0.467 ± 0.05) than the later stages (overall mean for adults, seedlings and juveniles H(e) = 0.438 ± 0.08). High gene flow was observed despite the fact that the fragmentation process began more than 100 years ago. We conclude that the high genetic diversity was the result of natural selection, which favours heterozygote excess in all stages, coupled with a combination of a reproductive system and seed/pollen dispersal mechanisms that favour gene flow.

Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability

Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied on to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase in up to 800% in comparison with the generally accepted maximum of 30-40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent or the Sp parameter. Consequently, we argue that greater standardization should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.

Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae)

PREMISE OF THE STUDY

Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii.

METHODS

We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each.

KEY RESULTS

All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high.

CONCLUSIONS

Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.

Spatial vs. temporal effects on demographic and genetic structures: the roles of dispersal, masting and differential mortality on patterns of recruitment in Fagus sylvatica

Trees' long lifespan, long-distance dispersal abilities and high year-to-year variability in fecundity are thought to have pervasive consequences for the demographic and genetic structure of recruited seedlings. However, we still lack experimental studies quantifying the respective roles of spatial processes such as restricted seed and pollen dispersal and temporal processes such as mast seeding on patterns of regeneration. Dynamics of European beech (Fagus sylvatica) seedling recruitment was monitored in three plots from 2004 to 2006. Six polymorphic microsatellite genetic markers were used to characterize seedlings and their potential parents in a 7.2-ha stand. These seedlings were shown to result from 12 years of recruitment, with one predominant year of seedling recruitment in 2002 and several years without significant recruitment. Using a spatially explicit mating model based on parentage assignment, short average dispersal distances for seed (δ(s) = 10.9 m) and pollen (43.7 m < δ(p) <57.3 m) were found, but there was also a non-negligible immigration rate from outside the plot (m(s) = 20.5%; 71.6% < m(p) < 77.9%). Hierarchical analyses of seedling genetic structure showed that (i) most of the genetic variation was within plots; (ii) the genetic differentiation among seedling plots was significant (F(ST) = 2.6%) while (iii) there was no effect of year-to-year seed rain variation on genetic structure. In addition, no significant effect of genetic structure on mortality was detected. The consequences of these results for the prediction of population dynamics at ecological timescales are discussed.

Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.

Spatial genetic structure within size classes of the endangered tropical tree Guaiacum sanctum (Zygophyllaceae)

PREMISE OF THE STUDY

Patterns of spatial genetic structure (SGS) were analyzed within a population of the endangered tropical tree Guaiacum sanctum located in northwestern Costa Rica. Documentation of these patterns provides insights into the gene dispersal mechanisms that play a central role in the maintenance and structure of genetic diversity within plant populations. •

METHODS

Allozyme analyses were used to examine SGS in Palo Verde National Park, Costa Rica. The SGS was compared among three plots and different age classes. •

KEY RESULTS

High levels of genetic diversity were found overall with a pooled genetic diversity of H(e) = 0.302 (±0.02). Selfing was proposed as the proximate cause for significant levels of heterozygote deficiency observed across size classes and plots. An unexpected lack of SGS (r(j) < 0.02) was observed for all size classes, suggesting the mixing of seeds from several adults. A parent-pair parentage analysis indicated that at least 48% of the smaller individuals within a plot were produced by parents located at distances of at least 150 m. •

CONCLUSIONS

Populations of G. sanctum are established and maintained by bird-mediated, moderate- to long-distance seed dispersal, which results in a mixture of seeds from unrelated maternal individuals, effectively eliminating SGS. Proximity between individuals is, therefore, a poor predictor of family structure in this species. Long-distance seed dispersal, coupled with estimates of high genetic diversity, suggests that this endangered species has the potential for natural regeneration and restoration given the availability of suitable habitats.

Natural selection drives the fine-scale divergence of a coevolutionary arms race involving a long-mouthed weevil and its obligate host plant

Background

One of the major recent advances in evolutionary biology is the recognition that evolutionary interactions between species are substantially differentiated among geographic populations. To date, several authors have revealed natural selection pressures mediating the geographically-divergent processes of coevolution. How local, then, is the geographic structuring of natural selection in coevolutionary systems?

Results

I examined the spatial scale of a "geographic selection mosaic," focusing on a system involving a seed-predatory insect, the camellia weevil (Curculio camelliae), and its host plant, the Japanese camellia (Camellia japonica). In this system, female weevils excavate camellia fruits with their extremely-long mouthparts to lay eggs into seeds, while camellia seeds are protected by thick pericarps. Quantitative evaluation of natural selection demonstrated that thicker camellia pericarps are significantly favored in some, but not all, populations within a small island (Yakushima Island, Japan; diameter ca. 30 km). At the extreme, camellia populations separated by only several kilometers were subject to different selection pressures. Interestingly, in a population with the thickest pericarps, camellia individuals with intermediate pericarp thickness had relatively high fitness when the potential costs of producing thick pericarps were considered. Also importantly, some parameters of the weevil - camellia interaction such as the severity of seed infestation showed clines along temperature, suggesting the effects of climate on the fine-scale geographic differentiation of the coevolutionary processes.

Conclusion

These results show that natural selection can drive the geographic differentiation of interspecific interactions at surprisingly small spatial scales. Future studies should reveal the evolutionary/ecological outcomes of the "fine scale geographic mosaics" in biological communities.

Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales)

The distribution of genetic diversity and structure for three populations of Dioon edule Lindley (Zamiaceae) at Monte Oscuro (MO), El Farallón (EF) and Rancho del Niño (RN) in Veracruz, Mexico was studied using 20 allozyme loci, considering four life history classes: seeds, seedlings, juveniles and adults. The MO population is genetically less diverse than the EF and RN populations. Total and local inbreeding differ significantly between life history classes. An increment of inbreeding among all classes was observed, and genetic differentiation among populations was higher in seeds and seedlings than in juveniles and adults. In terms of percentage of polymorphic loci, the MO seeds showed least (80%), followed by RN (95%) and EF had the highest values (100%), probably because of a reduction in effective population size and habitat fragmentation processes. In this context, the mean effective population size was 23.2 +/- 11.3 for all populations. We conclude that seed cohorts in EF and RN represent a reservoir of genetic diversity within these two populations. Also, preservation of adult plants is an essential aspect to consider in management and conservation efforts for populations of Dioon edule in natural conditions.

Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia

Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.

Demographic genetic structure of Cryptomeria japonica var. sinensis in Tianmushan Nature Reserve, China

Genetic changes over space and time provide insights into the relative roles of evolutionary factors in shaping genetic patterns within plant populations. However, compared with spatial genetic structure, few studies have been conducted on genetic changes over time. In this study, we used six polymorphic microsatellite loci to assess genetic variation of six size-classes of the population of Liushan, Cryptomeria japonica var. sinensis, in the Tianmushan National Nature Reserve, whose origin was debatable. The mean number of alleles per locus and expected heterozygosity were 4.583 and 0.599 9 respectively, lower than other conifers with the same life history characteristics. FST was 0.002+/-0.003, and the pairwise test revealed no significant differentiation in any pair of size classes. Significant heterozygosity excesses were detected in five size classes except the oldest one, indicating bottleneck event(s). The above results support the hypothesis that Tianmushan population was introduced and followed by natural regeneration.

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae)

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

A spatially explicit analysis of seedling recruitment in the terrestrial orchid Orchis purpurea

Seed dispersal and the subsequent recruitment of new individuals into a population are important processes affecting the population dynamics, genetic diversity and spatial genetic structure of plant populations. Spatial patterns of seedling recruitment were investigated in two populations of the terrestrial orchid Orchis purpurea using both univariate and bivariate point pattern analysis, parentage analysis and seed germination experiments. Both adults and recruits showed a clustered spatial distribution with cluster radii of c. 4-5 m. The parentage analysis resulted in offspring-dispersal distances that were slightly larger than distances obtained from the point pattern analyses. The suitability of microsites for germination differed among sites, with strong constraints in one site and almost no constraints in the other. These results provide a clear and coherent picture of recruitment patterns in a tuberous, perennial orchid. Seed dispersal is limited to a few metres from the mother plant, whereas the availability of suitable germination conditions may vary strongly from one site to the next. Because of a time lag of 3-4 yr between seed dispersal and actual recruitment, and irregular flowering and fruiting patterns of adult plants, interpretation of recruitment patterns using point patterns analyses ideally should take into account the demographic properties of orchid populations.

Demographic spatial genetic structure of the Neotropical tree, Jacaranda copaia

We used genotypes from six microsatellite loci and demographic data from a large mapped forest plot to study changes in spatial genetic structure across demographic stages, from seed rain to seedlings, juveniles, and adult diameter classes in the Neotropical tree, Jacaranda copaia. In pairwise comparisons of genetic differentiation among demographic classes, only seedlings were significantly differentiated from the other diameter classes; F(ST) values ranged from 0.006 to 0.009. Furthermore, only seedlings showed homozygote excess suggesting biparental inbreeding in the large diameter reproductive adults. We found very low levels of relatedness in the first distance class of trees, 1-26 cm diameter (F(ij) = 0.011). However, there was a 5- to 10-fold rise in relatedness in the smallest distance class, from the smallest to the largest tree diameter classes (F(ij) = 0.110 for individuals > 56 cm diameter). A variety of non-mutually exclusive mechanisms have been invoked perviously to explain such a pattern, including natural selection, history, or nonequilibrium population dynamics. The long-term demographic data available for this species allow us to evaluate these mechanisms. Jacaranda is a fast-growing, light-demanding species with low recruitment rates and high mortality rates in the smaller diameter classes. It successfully regenerates only in large light gaps, which occur infrequently and stochastically in space and time. These factors contribute to the nonequilibrium population dynamics and observed low genetic structure in the small size classes. We conclude that the pattern of spatial genetic transitions in Jacaranda is consistent with overlapping related generations and strong but infrequent periods of high recruitment, followed by long periods of population decline.

Fine-scale genetic structure of life history stages in the food-deceptive orchid Orchis purpurea

In natural plant populations, fine-scale spatial genetic structure can result from limited gene flow, selection pressures or historical events, but the role of each factor is in general hard to discern. One way to investigate the origination of spatial genetic structure within a plant population consists of comparing spatial genetic structure among different life history stages. In this study, spatial genetic structure of the food-deceptive orchid Orchis purpurea was determined across life history stages in two populations that were regenerating after many years of population decline. Based on demographic analyses (2001-2004), we distinguished between recruits and adult plants. For both sites, there was no difference in the proportion of polymorphic loci and expected heterozygosity between life history stages. However, spatial autocorrelation analyses showed that spatial genetic structure increased in magnitude with life history stage. Weak or no spatial genetic structure was observed for recruits, whereas adult plants showed a pattern that is consistent with that found in other species with a predominantly outcrossing mating system. The observed differences between seedlings and adults are probably a consequence of changes in management of the two study sites and associated demographic changes in both populations. Our results illustrate that recurrent population crashes and recovery may strongly affect genetic diversity and fine-scale spatial genetic structure of plant populations.

Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites

Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae)

BACKGROUND AND AIMS

For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes.

METHODS

Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones.

KEY RESULTS

A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones.

CONCLUSION

The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

How much genetic variation is stored in the seed bank? A study of Atriplex tatarica (Chenopodiaceae)

We investigated to what extent the soil seed bank differed genetically and spatially in comparison to three consecutive life history stages (seedlings, mature plants, and fruiting plants) in a natural population of Atriplex tatarica. Representatives of particular life history stages from twenty subunits within a large population were randomly collected and subjected to allozyme analysis. Comparison of population polymorphism among various life history stages showed significant differences in observed heterozygosity (H(O)) and F statistics (F(IS) and F(ST)), but nonsignificant ones in the cases of number of alleles per polymorphic locus (A) and gene diversity (H(S)). These results indicate an increasing number of heterozygotes, a decreasing level of inbreeding and an increase of the partitioning genetic diversity among populations with increasing population age. Spatial autocorrelation was used to calculate f, the average co-ancestry coefficient between individuals within distance intervals of two meters along a 39 m long transect. Significant positive fine scale genetic structure was detected in mature and fruiting plants but not in soil seeds and seedlings stages. The results of the presented study on A. tatarica indicated that significant differences exist in genetic differentiation, differentiation in allele frequencies and spatial autocorrelation among early (soil seeds and seedlings) and late (mature and fruiting plants) life history stages but not within early and late ones. This pattern suggests that, rather than storing genetic variability in the soil or germination and establishment success, self-thinning might be the major microselective force in populations of A. tatarica.

Inferring colonization history from analyses of spatial genetic structure within populations of Pinus strobus and Quercus rubra

Many factors interact to determine genetic structure within populations including adult density, the mating system, colonization history, natural selection, and the mechanism and spatial patterns of gene dispersal. We examined spatial genetic structure within colonizing populations of Quercus rubra seedlings and Pinus strobus juveniles and adults in an aspen-white pine forest in northern Michigan, USA. A 20-year spatially explicit demographic study of the forest enables us to interpret the results in light of recent colonization of the site for both species. We assayed 217 Q. rubra seedlings and 171 P. strobus individuals at 11 polymorphic loci using nine allozyme systems. Plant genotypes and locations were used in an analysis of spatial genetic structure. Q. rubra and P. strobus showed similar observed levels of heterozygosity, but Q. rubra seedlings have less heterozygosity than expected. Q. rubra seedlings show spatial genetic clumping of individuals on a scale to 25 m and levels of genetic relatedness expected from the clumped dispersion of half-siblings. In contrast, P. strobus has low levels of genetic relatedness at the smallest distance class and positive spatial genetic structure at scales < 10 m within the plot. The low density of adult Q. rubra outside the study plot and limited, spatially clumped rodent dispersal of acorns is likely responsible for the observed pattern of spatial genetic structure and the observed heterozygote deficit (i.e. a Wahlund effect). We attribute weaker patterns observed in P. strobus to the longer dispersal distance of seeds and the historical overlap of seed shadows from adults outside of the plot coupled with the overlap of seed shadows from younger, more recently established reproductive adults. The study demonstrates the utility of long-term demographic data in interpreting mechanisms responsible for generating contemporary patterns of genetic structure within populations.

Spatial genetic structure of two sympatric neotropical palms with contrasting life histories

The spatial genetic structure within sympatric populations of two neotropical dioecious palm species with contrasting life histories was characterized to evaluate the influence of life history traits on the extent of genetic isolation by distance. Chamaedorea tepejilote is a common wind-pollinated arboreal understory palm. Chamaedorea elatior is an uncommon climbing subcanopy palm with entomophilous pollination syndrome. A total of 59 allozyme alleles for C. tepejilote and 53 alleles for C. elatior was analyzed using both unweighted (Iu) and weighted (Iw) Moran's I spatial autocorrelation statistics. The spatial genetic structure detected within these populations is consistent with those reported for highly dispersed plants. A significance test for differences between mean Moran's I-coefficients revealed less spatial genetic structure within the C. tepejilote population than that in the C. elatior population. Adjacent individuals of C. elatior exhibited significant spatial genetic autocorrelation (Iu=0.039, Iw=0.034), indicating a Wright's neighborhood size of about 100 individuals. For C. tepejilote, nonrandom genetic distribution among nearest neighbors was detected, even from small spatial autocorrelation values (Iu=0.008, Iw=0.009), consistent with a neighborhood size of about 300 individuals. For both species, seed dispersal, mortality among life cycle stages, overlapping generations, and contrasting traits of mating and reproduction influence the standing spatial genetic structure within populations.

Imbalance of Predator and Prey Armament: Geographic Clines in Phenotypic Interface and Natural Selection

The escalation of defensive/offensive arms is ubiquitous in prey-predator evolutionary interactions. However, there may be a geographically varying imbalance in the armaments of participating species that affects the outcome of local interactions. In a system involving the Japanese camellia (Camellia japonica) and its obligate seed predator, the camellia weevil (Curculio camelliae), we investigated the geographic variation in physical defensive/offensive traits and that in natural selection on the plant's defense among 17 populations over a 700-km-wide area in Japan. The sizes of the plant defensive apparatus (pericarp thickness) and the weevil offensive apparatus (rostrum length) clearly correlated with each other across populations. Nevertheless, the balance in armaments between the two species was geographically structured. In the populations for which the balance was relatively advantageous for the plant's defense, natural selection on the trait was stronger because in the other populations, most plant individuals were too vulnerable to resist the attacks of the weevil, and their seeds were infested independent of pericarp thickness. We also found that the imbalance between the defensive/offensive armaments and the intensity of natural selection showed clear latitudinal clines. Overall, our results suggest that the imbalance of armament between sympatric prey and predator could determine the strength of local selection and that climatic conditions could affect the local and overall trajectory of coevolutionary arms races.

Temporal patterns of genetic variation across a 9-year-old aerial seed bank of the shrub Banksia hookeriana (Proteaceae)

The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P(p)) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (H(j)), did not change. P(p), I, and H(j) all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H(j) or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.

Estimating dispersal from short distance spatial autocorrelation

A series of theoretical studies has formed a strong connection between spatial statistics observed in populations and summary measures of the amount of dispersal. Synthesized, these developments allow dispersal to be indirectly estimated from standing spatial patterns of genetic variation under a range of conditions broad enough to be likely met in most populations of either plants or animals. The spatial correlations at the shortest distances are particularly robust to range of conditions and have disproportionately high statistical power. This review integrates theoretical results in a way that maximizes robustness and flexibility in the use of short distance autocorrelation to estimate Wright's neighborhood size, or the total variance in dispersal distances. Empirical guidelines are developed that are meant to be as practical and broad as possible. The guidelines focus on Moran's I-statistics for diploid genotypes converted to allele frequencies, but are also extended to or compared with several other approaches.