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Jolivet C, Holtken AM, Liesebach H, Steiner W, Degen B. Spatial genetic structure in wild cherry (Prunus avium L.): I. variation among natural populations of different density. Tree Genet Genomes 7: 271-283
Abstract
Conservation of forest genetic resources requires intensive knowledge of the spatial arrangement of genetic diversity. In
this study, we used four natural Prunus avium stands in Germany with contrasting for densities to understand patterns of spatial genetic structure. To this end, we genotyped
adults and saplings at eight microsatellite markers, 54 AFLP loci and at the gametophytic incompatibility locus. We estimated
levels of clonal propagation, spatial genetic structure and gene dispersal. High mortality occurred among young clonal individuals,
as depicted by the lower clonal diversity in saplings. Contrasting levels of spatial genetic structure were observed among
markers, ontogenic stages and populations. AFLP were more efficient for detecting spatial autocorrelation but did not allow
us to differentiate low and high density populations, while high density populations showed substantially stronger spatial
genetic structure at microsatellite loci. Furthermore, kinship decreased with tree age only in low density stands. We discuss
the present results in terms of population history, pollen and seed dispersal and population density. Although conspecific
density seems to be an interesting indicator of genetic diversity for conservation programmes, we still need to disentangle
the relative influence of clonal propagation and density on the strength of spatial genetic structure. Simulation studies
are needed to further address this question.
KeywordsSpatial genetic structure–Microsatellite–AFLP–Gametophytic incompatibility system–Density–Clonal propagation
... As a species with gametophytic self-incompatibility, P. avium maintains significant genetic variability through sexual reproduction (Ganopoulos et al., 2012 ). However, the intrapopulation variability of cherry stands is strongly reduced by vegetative propagation via root suckers and the formation of clonal groups (Schueler et al., 2006; Vaughan et al., 2007a; Jolivet et al., 2011; Jarni et al., 2012). The factors that impact genetic variability and population structure can be broadly divided into (1) general (direct) factors which relate to a species (or groups of species), e.g. ...
... Recent molecular marker studies have shown significant SGS for P. avium, which confirms the species' limited pollen and seed dispersal (Schueler et al., 2006; Vaughan et al., 2007a; Jolivet et al., 2011). Schueler et al. (2006) used microsatellite markers and S-alleles in Germany and found that P. avium trees in a stand are genetically more similar than expected by chance up to a distance of 85 m. ...
... Schueler et al. (2006) used microsatellite markers and S-alleles in Germany and found that P. avium trees in a stand are genetically more similar than expected by chance up to a distance of 85 m. Our study also confirms the strong and significant SGS of P. avium, which could be the consequence of substantial vegetative propagation in combination with high conspecific density (Jolivet and Degen, 2011 ). Indeed, at least 69 per cent of all analyzed trees in the stand have vegetative origin, and in addition, the MLL size (N R ) distribution (data not shown) and Pareto index (b ¼ 0.63) indicate dominance of some large clonal lineages and the additional presence of many small ones. ...
Microsatellite markers were used to describe the genetic structure of a natural wild cherry (Prunus avium L.)
stand in Slovenia. Based on eight analyzed loci, only 67 different multilocus genotypes (MLGs) were identified
among 217 trees, indicating a significant amount of clonal reproduction in the stand. Lowspatial genetic structure
(SGS) was observed in the stand when only sexually derived genets were considered (Sp ¼ 0.011), and the
kinship coefficient was only significant in the first distance class (,40 m).When both the generative and vegetative
origin of trees were included, the intensity of the SGS in the stand increased (Sp ¼ 0.149). Forest paths,
streams and ditches, which represent obstacles to root growth and consequently obstruct vegetative propagationvia
root suckers, also affected the spatial grouping of clones in the stand.Arelatively high numberof somatic
mutations within clonal groups were observed, which further increased the complexity of the genetic structure
in the stand.
... However, in order to ensure the usefulness of these species are maintained well into the future, protective measures must be taken now to secure their continuation prior to their projected range expansion. The current popular conservation methodology includes installing stepping-stones or otherwise increasing the connectivity of scattered Rosaceae populations (Dobeš et al., 2017;Cachi et al., 2017;Jolivet et al., 2011;Kamm et al., 2009;Kavaliauskas et al., 2021;Maděra et al., 2013;Oddou-Muratorio et al., 2003Schnitzler et al., 2014). However, many other viable conservation measures currently exist and would increase in their viability with the use of more defined targeted goals. ...
... First, the majority of papers (n = 138) promote further research to increase the amount of information available when designing management plans (e.g. Breitbach et al., 2010;Kišek et al., 2021;Jolivet et al., 2011). Second, many papers (n = 57) focus on increasing genetic exchange between populations with the goal of increasing genetic diversity and safeguarding against future bottleneck events (e.g. ...
Climate change is only continuing to advance, and so its effects are continuing to balloon. Within that, Rosaceae trees, with immense economic and ecological importance, are being variably impacted depending on their usability and niche association. Furthermore, genetic-based conservation is growing in popularity due to its ability to more accurately tailor conservation response plans. Because of this, it is important to understand where consensus lies among Rosaceae conservation research and to build starting points for conservation organizations and forest managers regarding Rosaceae preservation and restoration. In this review we aim to assess the consensus among 253 papers from 2001 to 2021 regarding threats, conservation, and management of wild and cultivated Rosaceae trees with wild populations in Europe. Through meta-analysis and thorough review to identify common themes, we identify varying levels of consensus. The most agreement lies in that environmental threats have largely genetic impacts, and that conservation should focus on more passive measures which ensure that future harm is mitigated and minimized. Therefore, continuing to understand the state of Rosaceae genetics and population connectivity will allow for the most comprehensive conservation and management plans to be developed in the coming years.
... This paradigm has not been truly resolved based on empirical studies. Several authors found evidence for spatial genetic structure at both the S-RNase locus and microsatellite markers, but they could not ascertain clear differences in the extent of spatial genetic structure between these types of loci (Jolivet et al., 2010;Schueler et al., 2006). The difference between spatial genetic structure at the S-locus and at unlinked neutral markers is expected to strongly depend on the number of S-alleles and on the distance of pollen and seed dispersal (Leducq et al., 2011), but other factors, such as population history and the degree of population fragmentation might also be important. ...
... There are only few studies on trees (mostly Prunus avium), where spatial genetic structure was assessed based on the S-RNase locus and neutral loci, such as microsatellites (Schueler et al., 2006;Jolivet et al., 2010). However, so far comparisons of SGS between the S-RNase locus and microsatellites have provided inconsistent results. ...
Distribution of genetic diversity among and within plant populations may depend on the mating system and the mechanisms underlying the efficiency of pollen and seed dispersal. In self-incompatible species, negative frequency-dependent selection acting on the self-incompatibility locus is expected to decrease intensity of spatial genetic structure (SGS) and to reduce population differentiation. We investigated two populations (peripheral and more central) of wild service tree (Sorbus torminalis (L.) Crantz), a self-incompatible, scattered tree species to test the differences in population differentiation and spatial genetic structure assessed at the self-incompatibility locus and neutral nuclear microsatellites. Although, both populations exhibited similar levels of genetic diversity regardless of the marker type, significant differentiation was noticed. Differences between F ST and R ST suggested that in the case of microsatellites both mutations and drift were responsible for the observed differentiation level, but in the case of the S-RNase locus drift played a major role. Microsatellites indicated a similar and significant level of spatial genetic structure in both populations; however, at the S-RNase locus significant spatial genetic structure was found only in the fragmented population located at the northeastern species range limits. Differences in SGS between the populations detected at the self-incompatibility locus were attributed mainly to the differences in fragmentation and population history.
... Wild populations of fruit trees are often affected by humans through overexploitation and fruit choice; this results in a loss of genetic diversity and structure. For these reasons, the conservation of wild resources has received increasing attention over the last decades (Jolivet et al. 2011). Transplanting wild fruit trees into a germplasm repository, or through shoot grafting, is conducive to qualitative and quantitative trait assessment, conservation, and usage, but is labor-intensive, costly, not always convenient (especially when collection locations are large distances from conservation sites), and also comes with an inherent risk of mortality (Richards et al. 2009). ...
... This allows the development of strategies for the management and exploitation of resources required to promote successful fruit breeding. Hence, knowledge of genetic diversity and population structure within the seedling population, after seed collection, is important for the successful use of resources (Jolivet et al. 2011). Similar studies have been carried out on other types of fruit tree. ...
Pyrus pashia, described as an intermediate species between oriental and occidental pear groups, is one of the most important wild pears. This study used microsatellite markers at 14 loci to assay genetic diversity and differentiation within P. pashia using three complementary methods. Four hundred and seventy seedlings were obtained from 38 half-sib families from four sites in the central Yunnan Province of China. These 14 loci displayed high polymorphism, and the descriptive statistics of diversity varied significantly among seedling populations. One hundred and seventy-three different alleles were detected, with an average of 12.4 alleles per locus. The overall expected and observed heterozygosity values were 0.749 and 0.643, respectively. Allelic richness at the different sites ranged from 1.00 to 20.36, and the Shannon’s information index for each locus was from 0.35 to 2.37, with a mean value of 1.82. Genetic differentiation was detected at both family and site levels using Bayesian model and neighbor-joining clustering approaches and the results compared with that of principal coordinate analysis. Two clusters, each with a similar number of families, were detected in the data set. Analysis of molecular variation indicated that the major variation occurred within families and that the minimum partitions of genetic variation exist among families, representing 89.14 and 10.86 % of the total variety, respectively. Families derived from site 2 displayed the maximum allelic richness and had a greatly mixed genetic composition. We recommend that these, especially families 9, 11, and 12, should be the focus of future preservation and usage investigations.
... Tree density and age class may also interact. In the study by Jolivet et al. (2011) on the wild cherry, Prunus avium, SGS was found to be more intense in saplings than adult trees, but only in low-density populations. Furthermore, SGS has been shown to vary across the geographical range of a species with SGS being absent in populations that are part of continuous forest distribution in the core region of the geographical distribution of Sitka spruce, Picea sitchensis despite being relatively strong elsewhere (Gapare and Aitken, 2005). ...
... The studies cited above demonstrate that variation in SGS within species can be substantial. Furthermore, such variation can be exacerbated by comparing across different molecular marker types, because the number of markers and degree of polymorphism of individual markers can also influence the results (Cavers et al., 2005; Jump and Peñuelas, 2007; Jolivet et al., 2011). Consequently, single estimates of SGS are unlikely to be reliable to accurately represent SGS for individual species. ...
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.
... Availability and informative value of plant germplasms are becoming more and more important for the future preservation and sustainable use of genetic resources [2]. However, this task is particularly challenging for trees whose life cycles are very long [3]. The importance of the research and conservation of local, traditional cultivars is evident, as this genetically heterogeneous material represents a potential source of positive pomological traits and resistance to biotic (including pests and diseases) and abiotic stress [4]. ...
In order to best conserve, as well as utilize, traditional apple germplasm in Norway, an apple heritage cultivar collection was established in Ullensvang, western Norway, which aims to become the National Clonal Germplasm Repository. The establishment of the apple heritage cultivar collection was preceded by a molecular study that aimed to genotype a large number of apple accessions maintained in various ex situ sites in western and south-eastern Norway, using a rather small set of eight SSR markers. However limited, the marker set managed to identify synonyms, homonyms, and duplicates within and among the investigated collections. In this study, 171 apple accessions from the Ullensvang apple heritage cultivar collection were genotyped using a set of 20 different SSR markers. Approximately half of the accessions have been previously genotyped using eight SSR markers, enabling an assessment of whether the use of a larger marker set would yield a more accurate characterization. Based on the obtained molecular data, the apple heritage cultivar collection was determined to hold a key part of the overall genetic diversity of the Norwegian apple germplasm. Furthermore, the twelve additional SSR markers were able to differentiate several accessions groups originally thought to be synonyms, as well as to provide a more detailed insight into the genetic structure of this germplasm.
... One of the very important elements of preserving the genetic diversity of Montenegrin forests is certainly the preservation and protection of wild fruit tree species. A comprehensive knowledge about the spatial pattern of genetic diversity is necessary for conservation of forest genetic resources (Jolivet et al. 2011). Spatial and species-specific variability of tree fruit in European forests have been poorly studied (Fernández-Martínez et al. 2017). ...
Wild fruit woody species without any doubt present an essential element of biodiversity of Montenegrin forests. The aim of this paper was to examine the geographical distribution of these species as a basic precondition for their monitoring and protection. According to the National Forest Inventory in Montenegro, there are seven wild fruit tree species present: chestnut (Castanea sativa Mill.), Turkish hazelnut (Corylus colurna L.), walnut (Juglans regia L.), wild apple (Malus sylvestris Mill.), wild cherry (Prunus avium L.) and wild pears (Pyrus communys L. and Pyrus amigdaliformis Vill.). Seven analyzed species are spread over an area of 9498 ha which takes up 0,69% of the territory of Montenegro. Most common wild fruit tree species in Montenegro are wild pear, wild cherry and wild apple. The highest values of average timber dimensions show wild cherry, chestnut and Turkish hazelnut. Further analysis of the distribution according to the altitude shows which species are located mainly on terrains of lower altitude and which species spread mainly at altitudes above 800 m and how altitude influenced the diversity of these species. Distribution and main characteristics of Montenegrin wild fruit tree species shows potential for establishment of collecting site areas as first step of in situ conservation.
... Significant FSGS in species with the SI system, which includes the black cherry, may negatively affect future population persistence and performance because the Allele effect may negatively affect mean fitness and thus lower the probability of invader establishment (Willi 2005). Our quantification of FSGS in this study was based on neutral genetic markers, and studies show that these may not follow the spatial structure of the S-RNase locus (Jankowska- Wroblewska et al. 2016;Jolivet et al. 2010). Hence, it seems that in invasive species with the SI system, including the S-RNase locus into investigations would provide more comprehensive insight into the mechanism governing the spatial distribution of genetic information and thus directions of population process relevant for invasive spread. ...
Prunus serotina Ehrh. (black cherry) is one of the most important invaders in the European forests, but existing studies have given limited insight into demo-genetic factors underpinning the process of species invasion. Fine-scale genetic structure (FSGS) may deliver important knowledge on genetics of invasion contributing to efficient management of the alien species. Using eight microsatellites we investigated FSGS, clonal structure and relatedness in four black cherry populations which represented different stages of the invasive spread into Scots pine forests. Three populations were in a continuous forest complex and represented the colonization (Z_1) and established stages (Z_2 and Z_3). To investigate how colonization ability of the species is modified by landscape features, we analyzed an isolated population at colonization stage located in limited forest patch located in an agricultural landscape (R). Populations from continuous forest showed low yet significant positive FSGS with Sp = 0.0068 in Z_1, 0.0054 in Z_2, and 0.0066 in Z_3, while in R spatial structure was the strongest (0.0145). Considerable relatedness noted in population R suggests a dominance of within-population mating and recruitments, low immigration rate and limited seed dispersal, all of which led to the observed strong FSGS. Also, we presume that a founder effect likely involved during colonization of isolated forest patch R led to strong FSGS. In contrary, the seed shadow overlap in the populations from continuous forest prevented strong FSGS and facilitated colonization. Despite of low level of clonality, we argue that it may efficiently support black cherry seedling bank contributing to species invasiveness. © 2018, Finnish Society of Forest Science. All rights reserved.
... This might mainly attribute to the various characters of marker systems. As pointed out by many recent studies in other species, microsatellite markers apparently could generate higher levels of genetic diversity for its hyper variability and higher resolving power among various genetic markers (Jolivet et al. 2011;Lacis et al. 2009;Zhou et al. 2003). ...
Chinese cherry (Cerasus pseudocerasus (Lindl). G. Don), native to China, is a commercially valuable fruit crop with extensive morphological diversity along Longmenshan Fault Zones, a region adjacent to the Qinling and Hengduan Mountains. In this study, we developed simple sequence repeat (SSR) markers from its own genome to comprehensively investigate the genetic variation of Chinese cherry in this center which is well-known by frequent geological activities and high levels of biodiversity. A total of 33,263 microsatellite sites were identified from the C. pseudocerasus genome, among which 30,148 SSR markers were designed. Of these markers, two hundred primer pairs were evaluated, and finally 20 polymorphic markers were selected to assess the genetic diversity and population structure of 15 representative natural populations (214 total individuals) in the region. The results revealed a moderately high genetic diversity in C. pseudocerasus (Na = 7.00, He = 0.62, PIC = 0.59, I = 1.26). A reduction of genetic variation, heterozygote excess and domestication bottleneck were detected in landrace populations (Na = 4.00, He = 0.41, Ar = 1.87, FIS = ?0.11) when compared with the wild ones (Na = 6.95, He = 0.65, Ar = 2.49, FIS = 0.35).The mantel test showed no significant correlation between geographic and genetic distance (r = 0.581, P = 0.08). Moderate differentiation and frequent gene flow were detected among all populations (FST = 0.0659, P = 0000, Nm = 3.5436). Nevertheless, a clear structure and relatively high differentiation (FST = 0.1173, P = 0000, Nm = 1.8813) were observed between most wild and landrace populations according to the STRUCTURE clustering and AMOVA analyses. The newly-developed SSR markers in our study exhibited high efficiency and can be utilized in further studies on this species and relatives. Meantime, the comprehensive assessments of genetic diversity of Chinese cherry resources in the biodiversity center have provided us basic genetic knowledge of this species, and this information will be very useful to policy makers on cherry breeding plan and species conservation.
... The Sp values in N. pumilio fit with the expected values for a wind pollinated species (Vekemans and Hardy, 2004). As proposed for fine-scale patterns of variation, the statistic should mirror the ecological features and demographic history of the species (Jolivet et al., 2011;Valbuena-Carabaña et al., 2007). Of particular relevance in our study is the higher and significantly different (from the other plots) Sp value detected in CF-Pop 3 (Lago del Engaño). ...
... This might mainly attribute to the various characters of marker systems. As pointed out by many recent studies in other species, microsatellite markers apparently could generate higher levels of genetic diversity for its hyper variability and higher resolving power among various genetic markers (Jolivet et al. 2011;Lacis et al. 2009;Zhou et al. 2003). ...
Chinese cherry (Prunus pseudocerasus Lindl.) is an ancient fruit crop with highly economic and ornamental values. It originated in China and the cultivation history can be traced back to 3,000 - 4,000 years ago. Over such a long-term domestication process, a large number of genetic variations have been accumulated in different landraces. However, their utilization for cultivar improvement is limited by the scarcity of information involving genetic diversity and population structure. Here, 17 populations comprised of 140 individuals were collected from four geographic areas: Sichuan Basin (SC), Qinglin Mountain (QL), Yungui Plateau (YG) and North of China (NC), and analyzed using a set of 20 microsatellite markers. In total, 126 polymorphic loci were generated, with 6.3 loci per primer. The global expected heterozygosity (He = 0.63) and Shannon information index (I = 1.23) implied a moderately high level of genetic variation. Two major clusters (cluster 1 and cluster 2) were demonstrated based on population structure analysis, which implied the presence of two potential domestication sites of Chinese cherry landraces. Individuals from SC were assigned to cluster 1 and those from QL, YG and NC were grouped into cluster 2. Samples from QL region contained the most plentiful admixture genetic components, implied the possibility of being one transition region of genetic variation. Moreover, botanical characteristics, such as long lifespan, inbreeding preference as well as vegetative propagation, might lead to a relatively low level but significant genetic divergence among populations. Finally, conservation strategies were proposed to protect these valuable natural germplasm based on these results.
... The cycling consisted of a denaturation step of 4 min at 94 °C, followed by 35 cycles of 25 s at 94 °C, 25 s at 60 °C (Set 1) and 56 °C (Set 2), respectively, and an extension of 45 min at 65 °C; the final extension took 45 min at 60 °C. We used a 25 µl PCR reaction mix for each sample as described in Jolivet et al. (2011). Amplified SSR fragments were analysed with an Amersham MegaBace 1000 capillary sequencer (GE Healthcare, Freiburg) and individual genotypes were determined with the Fragment Profiler software ver. ...
Over 30 Prunus species and taxa below the rank of species are known from Iran. These wild taxa provide an enlarged gene pool and may be considered a valuable germplasm source for breeding cultivated almonds. The present study is a genetic diversity analysis of six P. scoparia populations using six nuclear SSR markers. We also studied correlations between the population genetic differences, morphological differences and geographical distance. All six SSR primers produced amplification. The highest number of alleles occurred in the Fars and Lorestan populations, with 121 and 114 alleles, respectively. Some of the alleles were shared by all populations, while some others were specific to one population only. The observed heterozygosity ranged from 0.675 in the Tehran population to 0.900 in the Fars and Lorestan populations, while the expected heterozygosity ranged from 0.783 in the Tehran population to 0.948 in the Fars population. Bayesian model-based clustering showed a good separation of populations at K = 6. AMOVA indicated significant differences both among individuals and among populations. Mantel's test of SSR and morphological trees or geographical distance did not show any distinct pattern. Neighbour-joining and reticulation trees, as well as the STRUCTURE plots revealed admixture among the populations, indicating genetic exchange and presence of ancestral gene loci among them.
... Dies führt nachweislich zu einer höheren genetischen Differenzierung zwischen Vorkommen, was der Vergleich populationsgenetischer Ergebnisse verschiedener Studien eindeutig belegt (vgl. DEGEN et al., 2010;JOLIVET et al., 2011JOLIVET et al., , 2012REIM et al.. 2012). Unser Ergebnis der STRUCTURE-Analyse steht zum großen Teil auch in Einklang mit den zuvor schon von HUBER et al. (2013) gefundenen genetischen Abstandswerten zwischen den einzelnen Wildapfel-Vorkommen (gleicher Datensatz aus dem bundesweiten BLE-Projekt). ...
Conservation strategies for the indigenous European crab apple [Malus sylvestris (L.) Mill.], one of the forest botanical rarities in Europe, should imply ecological as well as genetic aspects. The decline of suitable habitats and the resulting reproductive isolation of relict stands imply the risk of extinction of the few remaining populations. In addition, low population sizes in combination with genetic introgression from apple cultivars involve the danger of losing wild type adaptive potential.
In the framework of a large project (2010-2013), funded by the Federal Office of Agriculture and Food, a nationwide inventory of ten rare native tree species has been carried out, among them the most important European crab apple populations. This unique data and sampling material was used to investigate the genetic resources by means of DNA markers.
This study demonstrates that population genetic methods enable to distinguish between European crab apple and apple cultivars as well as the proportion of admixture within hybrids. In addition to further population or phenological criteria, DNA-based methods turned out to be an interesting tool to detect wild type resources and to evaluate their need of protection.
Furthermore, we were able to group the existing crab apple gene pool within Germany into different reproductive units. This fact confirms the significance of provenances for the choice of wild type reproductive material in order to protect and to propagate adapted and adaptable populations of our European crab apple.
... They showed a higher differentiation than main tree species from which pollen can be transported by wind over large distances. The complexity of multiple mechanisms influencing spatial genetic structure is described in JOLIVET et al. (2011). The subpopulation in Saxony with the lowest d j -value (0.074) represents best the wild apple investigated in this study. ...
Malus sylvestris is the only apple species native to Central Europe. Its genetic integrity may be threatened by hybridization with the cultivated apple (Malus × domestica). A total of 883 genotypes, 477 putative wild apples in Germany and Luxembourg and 406 old to modern cultivars, has been investigated. Wild apples growing in Germany originated from Rhineland-Palatinate, North Rhine-Westphalia, Saxony-Anhalt and Saxony. The genetic structure was analysed at ten isozyme marker loci, and morphology was studied by fruit size, leaf pubescence, and a complex morphological description performed in advance. A model-based cluster analysis applied to all nuclear data resulted in two clearly differentiated gene pools for putative wild and cultivated apples with moderate proportions of admixture in the wild group on average (0.138 total, 0.111 German sample). At the individual level, the percentages of both hybrids and feral cultivars together ranged from 2.3% in Rhineland-Palatinate to 28.8% in Luxembourg. The intraspecific variability in fruit diameter ranged from 21 to 40 mm, and that in leaf pubescence in autumn ranged from score 0 to score 1. No single morphological trait of a specimen appeared to be sufficient for identification. Even the correspondence between the complex morphological and complex genetic determinations for individuals did not exceed 93% in pure wilds and 64% in hybrids. Genetic variation in pure wild apple is high (species level: P = 90%, A/L = 3.1, He = 0.369). Allelic differentiation δ was 0.089, pairwise genetic distance (d0) ranged from 0.065 to 0.148 among five samples. Correspondence between genetic and geographic distance of populations was observed to a certain extent.
... The availability and informative value of plant germplasm are becoming more and more important for the future preservation and sustainable use of genetic resources (Lacis et al., 2010). This task is particularly challenging in forest trees whose life cycles are very long (Jolivet et al., 2011). Since P. avium is widely distributed and has high level of genetic variability, which has not yet been well explored and exploited, ecotypes are expected to develop (Iezzoni, 2008 Since morphological characterization continues to be the first step for the description and classification of germplasm, numerous wild cherry genotypes have been evaluated and characterized for various traits, including diversity (Budan et al., 2009;Gregorius et al., 2011;Holtken and Gregorius, 2006;Ruisa, 1998;Stojecová and Kupka, 2009;Vaughan et al., 2007). ...
In thirty-three wild cherry (Prunus avium L.) accessions from Central Serbia, tree, leaf, fruit, and stone morphological characters were evaluated during three consecutive years. The goal was to detect relationships between the genotypes and to identify the most useful traits for discrimination among them. The study revealed a high variability in the set of the evaluated wild cherry accessions and considerable differences were found among them in all studied attributes. The majority of important correlations were determined among variables representing fruit and leaf size, and variables related to color. Cluster analysis distinguished wild cherry accessions into two distinct groups. In PCA, fruit and leaf traits such as leaf length and width, and fruit height, width, and weight, and skin flesh and juice color were predominant in the first two components, indicating that they were useful for the assessment of wild cherry germplasm characterization. These results indicate that these accessions must be conserved as valuable genetic resources to enrich the cherry gene pool and can be used for improving breeding efficiency of important horticultural traits worldwide.
... Ihre Zuordnungswahrscheinlichkeiten betrugen 100 % (Score: 1,000). Von den Samen aus dem Bestand Habichtshorst konnten nur 19 Individuen genotypisch erfasst wer- 1,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 G 0,000 1,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 H 0,000 0,000 1,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 B 0,000 0,000 0,641 0,359 0,000 0,000 0,000 0,000 0,000 0,000 0,000 R 0,000 0,000 0,000 0,000 1,000 0,000 0,000 0,000 0,000 0,000 0,000 Aa 0,000 0,000 0,000 0,000 0,000 1,000 0,000 0,000 0,000 0,000 0,000 Ab 0,000 0,000 0,000 0,000 0,000 0,000 1,000 0,000 0,000 0,000 0,000 Ka 0,000 0,000 0,000 0,000 0,000 0,000 0,000 1,000 0,000 0,000 0,000 Kb 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 1,000 0,000 0,000 Kc 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 1,000 0,000 SH 0,000 0,000 0,000 0,000 0,000 0,000 0,000 0,000 1,000 0,000 0,000 Degen et al. 2008;Jolivet et al. 2011Jolivet et al. , 2012reim et al. 2012). Damit sind noch aussagekräftigere Ergebnisse des Assignment-Ansatzes zu erwarten. ...
New regulations in landscaping using trees and shrubs of regional origin (§ 40 BNatSchG) require me thods for the identification of the geographical origin of its reproductive material. In this case study on pedunculate oak (Quercus robur L.) we present a DNA based procedure that enables the assign ment of seeds and young plant material to its origin stands of harvest. However, this method is not based on logistically complex and expensive systems of retaining samples that have to be taken and stored at each step of the chain-of-custody. For checking the origin of tree and shrub reproductive material, one inventory of the genetic structure of a seed production stand should be representative over a longer period of time as long as no distinct changes have been carried out in the structure of the populations.
... Die M13-Fingerabdruck-Methode bietet eine zuverlässige Möglichkeit zur genetischen Charakteri sierung von verschiedenen Individuen der gleichen Art (sie- (1) 1b Acer campestre (2) 1c Acer campestre (3) 1d Acer campestre (4) 1e Acer campestre (5) 1f Acer campestre (6) 2006;JOLIVET et al. 2011JOLIVET et al. , 2012REIM et al. 2012). Da die vor gestellten Methoden auch in anderen Bereichen, wie z. ...
Genetic analysis enables individual identifications of trees and shrubs, the development of methods to trace back plant material in the case of false labelling or investigation of damages caused by roots of trees. This individual genetic “barcodingprocedure” is performed by using the so called M13-fingerprinting method. A further technique is highlighted (microsatellites = SSRs) in order to control the varietal identity of offspring from specific individuals, crosses and breeding programs.
... In Romania, the differentiation calculated among four natural populations was relatively high ( F st = 0.156, Şo fl etea et al. 2008 ) . The genetic structure is also in fl uenced by the effects of human pressure such as silviculture and other effects (Jolivet et al. 2010 ) . In France, the genetic analyses allowed the establishment of only one large provenance region for this species. ...
Wild cherry ( Prunus avium L.) is one of the main hardwood species investigated
in Europe since the beginning of the 1980s. Wild cherry wood is highly sought
after for aesthetic applications such as panelling and cabinet-making, compared to
tropical wood s or other valuable European broadleaved species like walnut. In addition, the economic value is second only to walnut in the panorama of valuable European timbers.
Consequently, foresters’ interest in the species is ever increasing and the use of wild cherry has spread widely throughout Europe, from Great Britain to Italy, and from Spain to Eastern Europe. Breeding activities are here reported together with the mani features concerning the species.
With the contribution of: Joukje Buiteveld (Alterra, NL), Oscar Cisneros (JCYL, ES), Olivier Desteucq (CRNFB, BE), Raquel Díaz (Cifal, ES), Elena Foffova (NLC, SK), Helmut Grotehusman (NW-FVA, DE), Jan Kowalczic (IBL, PL), Dierk Kownazki (NFW, DE), Georghe Parnuta (ICAS, RO), Marijke Steenackers (INBO, BE), Lars-Göran Stener (Skogforsk, SE), Jan Svejgaard Jensen (FLD, DK).
... In Romania, the differentiation calculated among four natural populations was relatively high ( F st = 0.156, Şo fl etea et al. 2008 ) . The genetic structure is also in fl uenced by the effects of human pressure such as silviculture and other effects (Jolivet et al. 2010 ) . In France, the genetic analyses allowed the establishment of only one large provenance region for this species. ...
Wild cherry ( Prunus avium L.) is one of the main hardwood species investigated
in Europe since the beginning of the 1980s. Wild cherry wood is highly sought
after for aesthetic applications such as panelling and cabinet-making, compared to
tropical wood s or other valuable European broadleaved species like walnut. In addition, the economic value is second only to walnut in the panorama of valuable European timbers.
Consequently, foresters’ interest in the species is ever increasing and the use of wild cherry has spread widely throughout Europe, from Great Britain to Italy, and from Spain to Eastern Europe. Breeding activities are here reported together with the mani features concerning the species.
With the contribution of: Joukje Buiteveld (Alterra, NL), Oscar Cisneros (JCYL, ES), Olivier Desteucq (CRNFB, BE), Raquel Díaz (Cifal, ES), Elena Foffova (NLC, SK), Helmut Grotehusman (NW-FVA, DE), Jan Kowalczic (IBL, PL), Dierk Kownazki (NFW, DE), Georghe Parnuta (ICAS, RO), Marijke Steenackers (INBO, BE), Lars-Göran Stener (Skogforsk, SE), Jan Svejgaard Jensen (FLD, DK).
PREFACE (Authored by Michele Bozzano)
The genetic makeup of Forest Reproductive Material (FRM) is directly affected by the
decisions made by the various actors involved in its production chain. These decisions,
which often ignore the genetic perspective, have a major impact on the survival of future
forests.
There are still gaps and uncertainties in the current body of knowledge on the matter, such as which FRM should be recommended for a given site and what the adaptive potential of forest tree populations will be. This makes it difficult to prepare detailed guidelines for the production and use of FRM. These gaps are being partly addressed by ongoing research, which is generating scientific evidence to reinforce the development of decision support tools for assisting in the production and use of FGR.
In November 2015, the EUFORGEN Steering Committee established a working group to
unpack these research efforts and identify the genetic aspects in each link of the chain for the production and use of Forest Genetic Resources (FGR). The working group reviewed relevant literature and capitalised on the results of a previous EUFORGEN Network, known as the Forest Management network, which was active from 2005 to 2009.
. The group also built upon the publication, Use and transfer of forest reproductive
material in Europe in the context of climate change2
. Furthermore, the working group integrated
the discussion points derived from the GenTree3 stakeholders’ consultation which took
place in Madrid (Spain) in October 2016.The working group met three times: in November
2016 (Madrid, Spain), June 2017 (Warsaw, Poland) and November 2017 (Rome, Italy).
During the 13th Steering Committee meeting (June 2018), the draft report was presented
along with recommendations stemming from it for specific target groups. An extended
circle of experts from EUFORGEN community then received the document for peerreview. Finally, a Task Force (Katri Himanen (Finland), Paraskevi Alizoti (Greece) Sándor
Bordács (Hungary), Mari Mette Tollefsrud (Norway), Dušan Gömöry (Slovakia), Hojka
Kraigher (Slovenia) and Claes Uggla (Sweden)) reorganised the report in November 2018
(Oslo, Norway) and developed its first draft. In 2019 Silvio Oggioni, as a member of the
EUFORGEN Secretariat, contributed to the coordination and the finalisation of this report.
Several rounds of peer reviewing within the EUFORGEN community followed until June
2020.
This work is the result of an international collaboration rooted in EUFORGEN for more
than two decades. It is built on the firm belief that the genetic element is decisive for the
creation of a resilient forest capable of surviving threats and adapting to changes, thus
enabling the evolution of ecosystems and the conservation of the productive landscape.
Michele Bozzano,
EUFORGEN Coordinator,
December 2020
Fine-scale spatial genetic structure (SGS) is predominantly determined by gene flow. While sexually reproducing plants can disperse their genes through pollen and seed grains, clonal plants can additionally disperse genes through clonal growth. Plants' clonal reproduction strategy, however, often varies within and between species. Still, the effect of differential clonal reproduction strategy on fine-scale SGS remains somewhat unclear. Halophila ovalis is a fast-growing clonal seagrass, whose internode length (which defines a species' clonal reproduction strategy) varies among populations. Using eight polymorphic microsatellites, here we compare the genetic diversity, clonal structure and fine-scale SGS of two H. ovalis populations with contrasting internode lengths (Yingluo vs. Xialongwei populations). We found moderate to high genotypic and allelic richness and heterozygosities in both populations. Compared to Xialongwei population, genetic and genotypic diversity was significantly lower in Yingluo population. Although their internode length was relatively short, clones of Yingluo population spread farther than those of Xialongwei population. Sexual-to-vegetative dispersal variance ratios were 34.6 and 445.5 in Yingluo and Xialongwei populations, respectively. In both populations, clonal growth significantly intensified the SGS, especially in short distance classes. The SGS at small distance classes were weaker in Yingluo than Xialongwei, in part, due to more intermingled distribution of genets and more extensive clonal expansion in the former population. Our results indicate that vegetative dispersal variance/distance, rather than internode length, plays a crucial role in shaping the fine-scale genetic structure.
Assessing the population genetic structure of threatened species is important for developing successful conservation strategies. In this study, we evaluated the fine-scale spatial genetic structure (SGS) of Dalbergia nigra from a regenerating secondary forest fragment and compared it with previous data from a primary forest of a large reserve. A total of 107 adult and 111 saplings were mapped and genotyped for seven microsatellite loci. The genetic diversity was high and similar in adults (H
e = 0.682) and saplings (H
e = 0.680). The spatial extent of SGS was higher in adults than in saplings. Overlapping generations in the potentially reproductive individuals is the likely explanation for the higher SGS in adults (Sp = 0.016) in relation to the saplings (Sp = 0.010). The SGS in the adults from the secondary forest fragment was similar to that found in the primary forest. Considering the SGS found in adults, from both the secondary and primary forests, seeds for ex situ conservation should be collected from trees at least 80 m apart to reduce the genetic similarity between samples. These results highlight the importance of preserving small forest fragments to allow successful regeneration and maintenance of the genetic diversity in D. nigra.
Conservation of forest genetic resources has drawn much attention in the last decades, as it prevents negative effects of genetic erosion on adaptability potential of material used for afforestation. According to the German Act on Forest Reproductive Material, seed harvesting must occur in certified stands. Seed lots must stem from a minimum number of seed-trees, although the effect of this limit on genetic diversity has not been addressed. In this study, we aimed at understanding the effect of seed harvesting strategies on genetic diversity. We used the simulation model Eco-Gene and real molecular data to disentangle the effects of number of seed-trees and harvesting method in three wild cherry (Prunus avium) stands. Our results outline the importance of harvesting genetically different or distant seed-trees in maintaining genetic diversity. Besides optimal sampling strategy, we also recommend minimum harvesting of 25 seed-trees to reach 90 % of genetic diversity available within the stand. The outcomes of these results for the practice are also discussed.
Although pollen dispersal has been extensively studied in trees, parameters influencing between-population variation are still poorly understood. In this study, we conducted paternity analyses on open-pollinated seeds in four natural populations of wild cherry (Prunus avium) with contrasting density and clonal propagation, using eight microsatellite loci and one self-incompatibility system locus. We also measured four quantitative traits and spatial positions as potential correlates of reproductive success. Levels of polyandry differed among populations and 30% of the seed families exhibited unequal paternal contributions, suggesting variation in reproductive success rather than variation in mate availability. Mating occurred preferentially among neighbours in all populations, suggesting that it is a common pattern in wild cherry and probably results from pollinator behaviour. Paternal success was positively correlated with diameter at breast height, as indicated in previous studies and tree dominance only resulted in higher paternal success in low density plots. Mating patterns were thus also affected by both density and tree size. Large-scale studies are needed to disentangle relative influences of these factors on the mating system and pollination success.
Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.Heredity advance online publication, 5 December 2012; doi:10.1038/hdy.2012.103.
We conducted simulations to disentangle the effect of density and clonal propagation on spatial genetic structure and genetic
diversity parameters in Prunus avium. In a previous paper, we observed stronger family structure in populations exhibiting high density and high clonal propagation,
whereas one low-density and low clonal propagation population showed negative spatial autocorrelation. We tried to understand
these results by simulating 200years of growth, mating and dispersal with the model Eco-Gene, using two levels of density
and three levels of clonal propagation in one high-density population (Spargründe) and one low-density population (Chorin).
We used allele frequencies from eight microsatellite loci to generate the populations used for simulations. In order to detect
effects of the initial structure on the results, we also ran the simulations starting from the real data. We observed positive
effect of clonal propagation on the strength of SGS, while high densities exhibited a negative impact. Genetic diversity was
maintained at high densities, while pollen dispersal was shorter. Heterozygosity increased at higher clonal propagation rates,
although genetic diversity (accumulated number of genotypes) was lower. We discuss the results according to mating processes
and potential management scenario.
KeywordsSpatial genetic structure–Density–Clonal propagation–Simulation–Forest management–Genetic diversity
The restriction patterns of two chloroplast fragments and one mitochondrial DNA fragment, amplified by PCR with universal primers, were studied to determine the mode of inheritance of these organelles in 143 progeny of five intraspecific crosses in pedunculate oak (Quercus robur L.). The results indicate that both genomes are maternally inherited, an observation which agrees with the commonly observed pattern of inheritance in angiosperms. They confirm that both chloroplast DNA and mitochondrial DNA can be used as a source of seed-specific markers for the study of the geographic structure of oaks. This is the first report of organelle inheritance within the Fagaceae, an important and widespread tree family.
Several intensive wood production plantations and reafforestation programmes are being carried out in Europe using wild cherry (Prunus avium L.) as a valuable species. The study of the genetic structure of wild cherry managed and (or) unmanaged natural stands is important for resource management. Wild cherry stands are in fact frequently composed of single scattered trees or small dense groups, most of which are thought to have originated by suckering. Electrophoretic analysis of nine enzyme loci was carried out for five French managed stands and a unmanaged Italian stand. Phenological flowering phases were also assessed to confirm the presence of clonal sucker groups previously detected by electrophoresis within the Italian stand. Propagation by suckers was the most frequent propagation system; the number of genotypes detected within the examined populations varied from 6% to 49% of the total number of individuals. It particularly seems to occur within short distances and during the early successional stages. The following conclusions were thus drawn: the minimum distance between trees selected for improvement is 100 m; selective thinnings within wild cherry stands should take into account this minimum distance; mixtures of at least 5 to 10 clones, mostly from different origins, should be used in plantations, in order to improve heterogeneity and self-sustainability.
The spatial distribution of alleles is described in a forest stand of natural origin of 5 ha comprising 355 mature Quercus petraea and Q. robur trees. Each tree was genotyped for six microsatellite loci. Previous studies on the same population based on isozymes allowed a comparison of different markers for the detection of spatial genetic structure. Different statistics were used: differentiation measures at different spatial scales, and spatial autocorrelation analysis based on Moran's index I. For microsatellites, differentiation and autocorrelation were calculated with unordered alleles (identity in state) and with alleles ordered according to their size. Results showed the same tendency of a significant, but low, spatial genetic structure for markers and different statistics. Some differences could, however, be detected. First, microsatellites interpreted as unordered alleles exhibit stronger spatial structure than isozymes or microsatellite interpreted as ordered alleles. Second, differentiation and autocorrelation values were higher in Q. petraea than in Q. robur. These differences were attributed to species differences in gene flow via pollen or seed.
We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers.
Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad
scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits.
Seed dispersal mechanisms should have a direct impact on the genetic structure of populations. Species whose seeds are dispersed near the maternal plant (e.g. gravity or wind dispersal) or species whose seeds are deposited in clumps or patches should have more fine-scale genetic structure than species whose seeds are dispersed singly by mobile animals. Furthermore, due to the overlap of seed shadows, species with high adult densities should have less genetic structure than species with lower densities. Allozyme analyses of three tropical tree species belonging to the moist tropical forest of Barro Colorado Island, Republic of Panama, were used to describe variation in the scale and intensity of genetic structure within their populations. The genetic structure of seedlings and immature trees in the low-density, wind-dispersed species (Platypodium elegans) was the coarsest and strongest whereas genetic structure in a population of Swartzia simplex var. ochnacea (high density, bird-dispersed) was both the finest and the weakest. The genetic structure of Alseis blackiana, a high-density, wind-dispersed species was intermediate in both degree and scale. In P. elegans and A. blackiana, which had J shaped size distributions, the significant genetic structure seen in the smaller and intermediate diameter classes disappeared in the largest diameter class. The loss of genetic structure was not observed in S. simplex, a species with a more even size distribution.
Analyses of fine-scale and macrogeographic genetic structure in plant populations provide an initial indication of how gene flow, natural selection, and genetic drift may collectively influence the distribution of genetic variation. The objective of our study is to evaluate the spatial dispersion of alleles within and among subpopulations of a tropical shrub, Psychotria officinalis (Rubiaceae), in a lowland wet forest in Costa Rica. This insect-pollinated, self-incompatible understory plant is dispersed primarily by birds, some species of which drop the seeds immediately while others transport seeds away from the parent plant. Thus, pollination should promote gene flow while at least one type of seed dispersal agent might restrict gene flow. Sampling from five subpopulations in undisturbed wet forest at Estacion Biologica La Selva, Costa Rica, we used electrophoretically detected isozyme markers to examine the spatial scale of genetic structure. Our goals are: 1) describe genetic diversity of each of the five subpopulations of Psychotria officinalis sampled within a contiguous wet tropical forest; 2) evaluate fine-scale genetic structure of adults of P. officinalis within a single 2.25-ha mapped plot; and 3) estimate genetic structure of P. officinalis using data from five subpopulations located up to 2 km apart. Using estimates of coancestry, statistical analyses reveal significant positive genetic correlations between individuals on a scale of 5 m but no significant genetic relatedness beyond that interplant distance within the studied subpopulation. Multilocus estimates of genetic differentiation among subpopulations were low, but significant (F-st = 0.095). Significant F-st estimates were largely attributable to a single locus (Lap-2). Thus, multilocus estimates of F-st may be influenced by microgeographic selection. If true, then the observed levels of IBD may be overestimates.
Abstract spagedi version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling. spagedi is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.
Understanding the role of mother plants as pollen recipients in shaping mating patterns is essential for understanding the evolution of populations and in particular to predict the consequence of habitat fragmentation. Here, we investigated variation in mating patterns due to maternal phenotypic traits, phenological variance, and landscape features in Sorbus torminalis, a hermaphroditic, insect-pollinated and low-density, European temperate forest tree. The diversity and composition of pollen clouds received by maternal trees in S. torminalis were mainly determined by their conspecific neighborhood: isolated individuals sample more diversity through more even paternal contributions, low relatedness among paternal genes, and high rates of long-distance pollen dispersal within their progenies. Maternal phenotypic traits related to pollinator attractiveness also had an effect, but only when competition was strong: in this case, larger mother trees with more flowers sampled more diversity. The floral architecture of S. torminalis, with multiple-seeded fruit, strongly shaped mating patterns, with higher levels of correlated paternity among seeds belonging to the same fruit (30% full sibs) than among seeds belonging to different fruits (14% full sibs). Finally, flowering phenology affected the distribution of diversity among maternal pollen clouds, but the earliest and latest mother trees did not receive less diversity of pollen than the others.
Conversion of lowland woodland to agricultural land and resulting fragmentation in Britain has been ongoing since Neolithic times. To counteract this decline, plantations of native species, often based on non-British planting stock, have been established. This may ultimately be detrimental to the integrity of the native gene pool. We explore the genetic and ecological factors influencing the success of components of the local pollen pool, including the effect of a non-native planting on an ancient woodland population of wild cherry. Wild cherry exhibits gametophytic self-incompatibility (GSI) and vegetative reproduction, both of which may be determinants of paternal success. The majority (61%) of the successful pollen originated from within the study site with a maximum pollen transfer distance of 694 m. There was a distinct departure from random mating, with over half the successful pollen originating from trees which occur within 100 m of the mother tree. Self-incompatibility, clonality, tree size and proximity to the mother tree were all found to influence paternal success. Kinship of pollen gametes within a maternal progeny was highest when a mother tree was surrounded by a large number of ramets of a single, compatible clone consisting of large, adult trees. Although the contribution from the non-native plantation is currently low, it is likely that this will increasingly contribute to the progeny of the adjacent ancient population as it matures. The results clearly show that in self-incompatible species, such as P. avium, close neighbours may be pollinated by very different components of the local pollen pool.
Genetic structuring in response to the glacial cycles has been investigated for many plant species, but exclusively high-arctic ones have not been studied. Such extremely cold-adapted species have probably experienced range reductions under the present climate. Here we compare three predominantly selfing species of Draba with different distributions and hardiness (D. subcapitata, high-arctic; D. nivalis, arctic to arctic-alpine; D. fladnizensis, arctic-alpine) for genetic structuring on the basis of two different types of molecular markers (10 microsatellite loci and 160 amplified fragment length polymorphisms (AFLPs)). The degree of genetic structuring within these species is of particular interest because it has been shown that they contain many cryptic biological species. The high-arctic D. subcapitata had less phylogeographic structure, less diversity and fewer private alleles than the other two species, suggesting that long-distance dispersal may occur more frequently in the high arctic, that hardy plants may have higher probability for establishment after dispersal under high-arctic conditions and that high-arctic species may have experienced a bottleneck during the present interglacial. In contrast, D. fladnizensis and D. nivalis showed distinct phylogeographic structure and more diversity, suggesting separate long-term refugia in Eurasia and North America/Beringia. The AFLP markers revealed more phylogeographic structuring than the microsatellites, possibly because of the higher number of loci surveyed and/or because structure at very large geographic scales is blurred by high mutation rate leading to homoplasy at microsatellite loci. The number of genetic groups detected was in any case insignificant compared with the numerous cryptic biological species known within these species, supporting rapid development of sterility barriers.
A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification
of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA
and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis
of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site
sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into
the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the
restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide
sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments
that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50—100 restriction
fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful
DNA fingerprinting technique for DNAs of any origin or complexity.
I reexamine the use of isolation by distance models as a basis for the estimation of demographic parameters from measures of population subdivision. To that aim, I first provide results for values of F-statistics in one-dimensional models and coalescence times in two-dimensional models, and make more precise earlier results for F-statistics in two-dimensional models and coalescence times in one-dimensional models. Based on these results, I propose a method of data analysis involving the regression of FST/(1-FST) estimates for pairs of subpopulations on geographic distance for populations along linear habitats or logarithm of distance for populations in two-dimensional habitats. This regression provides in principle an estimate of the product of population density and second moment of parental axial distance. In two cases where comparison to direct estimates is possible, the method proposed here is more satisfactory than previous indirect methods.
Fully mapped tree census plots of large area, 25 to 52 hectares, have now been completed at six different sites in tropical
forests, including dry deciduous to wet evergreen forest on two continents. One of the main goals of these plots has been
to evaluate spatial patterns in tropical tree populations. Here the degree of aggregation in the distribution of 1768 tree
species is examined based on the average density of conspecific trees in circular neighborhoods around each tree. When all
individuals larger than 1 centimeter in stem diameter were included, nearly every species was more aggregated than a random
distribution. Considering only larger trees (≥ 10 centimeters in diameter), the pattern persisted, with most species being
more aggregated than random. Rare species were more aggregated than common species. All six forests were very similar in all
the particulars of these results.
We isolated and sequenced 26 microsatellites from two genomic libraries of peach cultivar 'Redhaven', enriched for AC/GT and AG/CT repeats, respectively. For 17 of these microsatellites, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was assayed in 50 peach and nectarine cultivars. Of the 1300 PCRs carried out, all but two produced amplified products of the expected size. All microsatellites were polymorphic, showing 2-8 alleles per locus. Heterozygosity ranged from 0.04-0.74 (mean 0.47); the discrimination power (PD) ranged from 0.04-0.84 (mean 0.60). Cultivar heterozygosity varied greatly, with one cultivar ('Independence') being homozygous at all loci. The set of microsatellites discriminated all cultivars investigated, except several sport mutations, i.e., 'Dixitime' vs. 'Springcrest', 'Compact Redhaven' vs. 'Redhaven', and two pairs of cultivars, 'Venus' vs. 'Orion' and 'Elegant Lady' vs. 'Rome Star', whose pedigrees are controversial. We were able to analyze the paternity of several cultivars. In most cases, the parenthood was confirmed. The comparison of three long-living 'Redhaven' accessions supplied by different repositories did not provide any evidence of somatic instability of microsatellites. Hence, microsatellites, ranked according to their information content, are recommended as markers of choice for peach fingerprinting and suggestions are provided for interpreting band profiles and the correct sizing of alleles.
The cane toad (Bufo marinus) was introduced in 1935 in Australia, where it spread rapidly. We have tested for isolation by distance by analysing at a local geographical scale a continuous population using seven microsatellite markers and an individual-based method. The matrix of pairwise individual differentiation was not significantly correlated with that of geographical distance. Regression analyses gave a low positive slope of 0.00072 (all individuals) or a negative slope of 0.0017 (individuals with a distance higher than the previously estimated mean dispersal distance). The absence of evidence for isolation by distance favours the hypothesis that the substantial differentiation and autocorrelation previously observed at enzyme loci, mainly results from discontinuities in the colonization process with founder effects occurring at the time of the establishment of new populations.
We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and F(ST) values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.
We report the sequence of 41 primer pairs of microsatellites from a CT-enriched genomic library of the peach cultivar 'Merrill O'Henry'. Ten microsatellite-containing clones had sequences similar to plant coding sequences in databases and could be used as markers for known functions. For microsatellites segregating at least in one of the two Prunus F(2) progenies analyzed, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was evaluated in 27 peach and 21 sweet cherry cultivars. All primer pairs gave PCR-amplification products on peach and 33 on cherry (80.5%). Six PCR-amplifications revealed several loci (14.6%) in peach and eight (19.5%) in sweet cherry. Among the 33 single-locus microsatellites amplified in peach and sweet cherry, 13 revealed polymorphism both in peach and cherry, 19 were polymorphic only on peach and one was polymorphic only on cherry. The number of alleles per locus ranged from 1 to 9 for peach and from 1 to 6 on sweet cherry with an average of 4.2 and 2.8 in peach and sweet cherry, respectively. Cross-species amplification was tested within the Prunus species: Prunus avium L. (sweet cherry and mazzard), Prunus cerasus L. (sour cherry), Prunus domestica L. (European plum), Prunus amygdalus Batsch. (almond), Prunus armeniaca L. (apricot), Prunus cerasifera Ehrh. (Myrobalan plum). Plants from other genera of the Rosaceae were also tested: Malus (apple) and Fragaria (strawberry), as well as species not belonging to the Rosaceae: Castanea (chestnut tree), Juglans (walnut tree) and Vitis (grapevine). Six microsatellites gave amplification on all the tested species. Among them, one had an amplified region homologous to sequences encoding a MADS-box protein in Malus x domestica. Twelve microsatellites (29.3%) were amplified in all the Rosaceae species tested and 31 (75.6%) were amplified in all the six Prunus species tested. Thirty three (80.5%), 18 (43.9%) and 13 (31.7%) gave amplification on chestnut tree, grapevine and walnut tree, respectively.
Nuclear microsatellites were characterized in Prunus avium and validated as markers for individual and cultivar identification, as well as for studies of pollen- and seed-mediated gene flow. We used 20 primer pairs from a simple sequence repeat (SSR) library of Prunus persica and identified 7 loci harboring polymorphic microsatellite sequences in P. avium. In a natural population of 75 wild cherry trees, the number of alleles per locus ranged from 4 to 9 and expected heterozygosity from 0.39 to 0.77. The variability of the SSR markers allowed an unambiguous identification of individual trees and potential root suckers. Additionally, we analyzed 13 sweet cherry cultivars and differentiated 12 of them. An exclusion probability of 0.984 was calculated, which indicates that the seven loci are suitable markers for paternity analysis. The woody endocarp was successfully used for resolution of all microsatellite loci and exhibited the same multilocus genotype as the mother tree, as shown in a single seed progeny. Hence, SSR fingerprinting of the purely maternal endocarp was also successful in this Prunus species, allowing the identification of the mother tree of the dispersed seeds. The linkage of microsatellite loci with PCR-amplified alleles of the self-incompatibility locus was tested in two full-sib families of sweet cherry cultivars. From low recombination frequencies, we inferred that two loci are linked with the S locus. The present study provides markers that will significantly facilitate studies of spatial genetic variation and gene flow in wild cherry, as well as breeding programs in sweet cherry.
Dicorynia guianensis is a canopy tree, endemic to the tropical rain forest of French Guiana. We compared generational and spatial genetic structure for maternally and biparentally inherited markers in two cohorts (adult and seedling) in order to infer processes shaping the distribution of genetic diversity. The study was conducted on a 40 ha study plot located at Paracou near Kourou, where 172 adults trees and 375 saplings were sampled. Aggregation of trees was therefore suggested at different distances, ranging from 100 to 400 m. There was a strong link between demographic and genetic spatial structures at small distances (less than 100 m) that is likely to be the consequence of restricted seed dispersal. Genetic differentiation was more pronounced between spatial aggregates than between cohorts. Despite the spatial differentiation, the species was able to maintain high levels of diversity for maternal genomes, suggesting rapid turnover of aggregates. Spatial autocorrelation was larger for chloroplast than nuclear markers indicating a strong asymmetry between pollen and seed flow. Fixation indices indicated a lower heterozygote deficiency for the adults, maybe because of gradual elimination of selfed trees. Genetic relatedness at lower distances was higher in adult trees than in saplings, as a result of generation overlapping in the adult cohort. Overall, our results confirm earlier biological knowledge about the dispersion mechanisms of the species, and lead to an enhanced role of spatial processes in the dynamics of genetic diversity of D. guianensis.
Spatial genetic structure was analysed with five highly polymorphic microsatellite loci in a Romanian population of common ash (Fraxinus excelsior L.), a wind-pollinated and wind-dispersed tree species occurring in mixed deciduous forests over almost all of Europe. Contributions of seed and pollen dispersal to total gene flow were investigated by analysing the pattern of decrease in kinship coefficients among pairs of individuals with geographical distance and comparing it with simulation results. Plots of kinship against the logarithm of distance were decomposed into a slope and a shape component. Simulations showed that the slope is informative about the global level of gene flow, in agreement with theoretical expectations, whereas the shape component was correlated with the relative importance of seed vs. pollen dispersal. Hence, our results indicate that insights into the relative contributions of seed and pollen dispersal to overall gene flow can be gained from details of the pattern of spatial genetic structure at biparentally inherited loci. In common ash, the slope provided an estimate of total gene dispersal in terms of Wright's neighbourhood size of Nb = 519 individuals. No precise estimate of seed vs. pollen flow could be obtained from the shape because of the stochasticity inherent to the data, but the parameter combinations that best fitted the data indicated restricted seed flow, sigmas pound 14 m, and moderate pollen flow, 70 m pound sigmap pound 140 m.
Camellia japonica L. (Theaceae), an insect- and bird-pollinated, broad-leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L-shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F-statistics, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m × 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's I-statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisita's index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self-thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self-thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.
We used allozyme loci, join-count statistics, and Moran's spatial autocorrelation statistics to quantify the spatial genetic structure caused by clonal reproduction from that maintained in sexually reproduced individuals in a population of distylous shrub Abeliophyllum distichum, a monotypic genus endemic to the central Korea. The population harbors high levels of multilocus genotypic diversity (mean DG = 0.960). Join-count statistics showed that there were statistically significant clustering of clonal genotypes within distances < 6 m. Both the entire population and the set of sexually reproduced individuals exhibited significant spatial autocorrelation up to the scale of about < 10 m, and the sexually reproduced individuals are in a substantially structured, isolation by distance, manner. This indicated that gene flow would not be extensive in a population of A. distichum because of pine forest acting as a shield for wind movement. Probable unequal ratio of the two floral morphos, selfing via matings between clones, and/or consanguineous matings may be factors for decreasing seed sets observed in the populations of the species ("inbreeding depression").
It is recommended that the sampling for conservation purposes might be performed at a diameter of more than 13 m to extract the genetic diversity across an entire population.
Allozymes were used to study the spatial attributes of clones (genets) comprising a population of Pteridium aquilinum var. latiusculum in the Appalachian Mountains of Virginia. Ramets (individual leaves) were genotyped for six polymorphic isozyme loci to produce a map depicting the spatial patterning of genets. Forty-five distinct genotypes were detected, 14 of which were sampled more than once, five of these more than four times. Genotype proportions at all loci except Pgm-1 conformed to Hardy-Weinberg expectations. Some genotypes represented by widely separated ramets have very low probabilities of re-encounter, documenting fragmentation of widespread genets. Coarse-scale mapping indicated a population consisting of many small genets and a few very large ones (up to 1015 m across). The larger genets tended to be irregular in shape, fragmented, and overlapping. Fine scale mapping of individual fronds in spatially discrete patches of ramets revealed extensive intergrowth of genets, indicating that P. aquilinum exhibits a "guerrilla-type' clonal morphology. -from Authors
Sicily has extensive germplasm of diploid sweet cherry (Prunus avium L.) that has not been well studied. In this investigation, 39 cherry accessions, selected from collections and farms, were analysed using molecular markers and characterised for various morphological and other agronomic characters such as flesh colour, fruit size, quality and, in some cases, ripening periods.Thirteen Simple Sequence Repeat (SSR) primer pairs, as well as two primer pairs for the incompatibility (S) locus, which amplified across the first intron of the S-RNase gene and across the intron of the SFB gene, were used in three multiplexed reactions to analyse the accessions.The number of alleles per SSR locus ranged from four to 11 (mean 7.2). Twelve S-alleles were found. Allele S4, which has been reported to be common in sweet cherry, was absent from the Sicilian germplasm and alleles S16 and S22 were frequent, although previously reported largely in wild populations.The accessions were assigned to their incompatibility groups.A UPGMA dendrogram was constructed and revealed possible synonyms. The set of SSR primers amplified unique fingerprints for 27 accessions, while twelve fell into six non-distinguishable groups. This approach could be used for comparing cultivars and wild
accessions from other regions, and for establishing a database of this important species for breeding and conservation purposes. Several accessions useful for breeding are reported.
An important aspect of the sustainable management of tropical rain forests is the maintenance of genetic diversity within populations of commercial tree species. Logging may reduce genetic variation directly and may also affect genetic processes, leading possibly to genetic erosion and ultimately even species extinction. It is, however, impractical for the forest manager to make meaningful measurements of genetic variation and they are therefore inappropriate for use as indicators of sustainable forest management. We propose that the application of well-known silvicultural principles is the most practical way of preventing rapid loss of genetic diversity. Most tropical rain forest tree species have many more individuals below the minimum size for commercial exploitation than above. The genetic diversity of these species will be little affected by logging, as the stems removed form only a small fraction of the total population. Similarly, for most species, disruption of normal mating patterns will either not occur or be transient, because reproduction commences at sizes well below felling limits, or because, after logging, juveniles will be recruited to the sexually mature size classes. Strongly light-demanding species with a commercial value are most likely to suffer loss of genetic diversity from logging. Characteristically, these have populations in which only a small proportion of the total population lies in small size classes. In order to conserve genetic diversity, pre-felling silvicultural treatments will be required to increase the survival and growth of juveniles. Ecological and genetic research needs to focus on these light-demanding species. # 2001 Elsevier Science B.V. All rights reserved.
The degree of canopy closure can shape the dynamics of understorey plant populations that rely on clonal and sexual recruitment. Populations are expected to undergo declines in clonal diversity under conditions where recruitment from seed is temporally and spatially restricted. Localized seedling recruitment in clonal populations may also affect spatial genetic structure due to the clumping of genetically related genets.
Our major objective was to determine the effect of the degree of canopy closure on clonal diversity and spatial genetic structure in the rhizomatous, dioecious forest perennial Mercurialis perennis . As the distribution of the male and female shoots has been shown to be influenced by canopy openings, we paid special attention to the mediating role of the varying sex ratio.
We used genome‐wide AFLP markers to fingerprint six populations of M. perennis along a light penetration gradient.
The proportion of male shoots in a population increased from 0.51 to 0.81 and male genet diversity decreased from 0.72 to 0.21 with increasing site illumination, in agreement with earlier reports of superior male growth in canopy openings. The most illuminated population, with the highest proportion of male shoots, was dominated by a few outsized, largely aggregated male clones (largest clone spreading over 10 m).
Overall clonal diversity (G/N: 0.31–0.74; mean: 0.52) and evenness strongly declined in well‐lit sites, suggesting reduced sexual recruitment and the vast vegetative spread of a few locally well‐adapted male genets under canopy gaps.
Fine‐scale genetic structure among genets was significant within all populations, but its degree tended to increase with an increased proportion of male shoots and reduced clonal diversity. Very localized recruitment due to a low seed dispersal capacity combined with the aggregated distribution of large gender‐specific clones likely incurred this pattern.
Synthesis. Forest management practices such as the cutting and removal of trees and the establishment of paths decreased the degree of canopy closure. Many understorey herb populations flourish in these canopy gaps, reflected in a higher clonal diversity. We demonstrated, however, that increased illumination negatively affects genotypic and genetic diversity in the dioecious understorey herb M. perennis .
— The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative F1T for the R stage). Spatial autocorrelation was used to calculate f, the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f= 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.
In plant populations exhibiting gametophytic self-incompatibility, individuals harbouring rare S alleles are likely to have a reproductive advantage over individuals having more common alleles. Consequently, determination of the self-incompatibility haplotype of individuals is essential for genetic studies and the development of informed management strategies. This study characterises six new S alleles identified in wild cherry (Prunus avium L.). Investigations to determine the S genotype of individuals in recently planted woodland through length polymorphisms of introns associated with the stylar S-RNase gene and the pollen SFB gene revealed six S intron profiles which did not correspond to those of known S alleles. These are now attributed to S
27
to S
32
. Consensus primers, annealing in the S-RNase sequence coding for the signal peptide and C5 regions, were used to isolate the S-RNase alleles associated with the novel S intron profiles. The proteins corresponding to the new alleles were separated by isoelectric focusing from stylar extracts and their pI values determined. Similarities between the deduced amino acid sequence for the new alleles isolated and other cherry S-RNase sequences available on the databases ranged from 40% to 86%. Amplification products for SFB introns ranged from 172 to 208bp. New sequence regions exposed to positive selection were identified and the significance of the PS3 region reinforced. A phylogenetic relationship between P. avium S-RNases for S
10
and S
13
and between corresponding SFB alleles may indicate co-evolution of allele specificities of these two genes.
Steady reduction of once-extensive forested habitats into isolated fragments will have unintended consequences for genetically disrupted tree populations. Gene flow in forest trees involves both pollen and seed flow, and here we describe two alternative analytical models for pollen flow analysis, PARENTAGE and TWOGENER. With PARENTAGE models, we can assess the numbers and frequency spectra of pollinating males for a single female, and the spatial distribution of those pollinating males. Parentage analysis establishes the male parentage of offspring, and uses the inter-parent distances to establish the spatial distribution of pollination. With TWOGENER analysis, we gauge the degree of pollen pool non-overlap of widely spaced females, to derive estimates of the effective number of fathers per mother and the average distance of pollination. Parentage analysis suggests large numbers of fathers per mother while TWOGENER analysis suggests smaller numbers of ‘effective pollinators’. Because of TWOGENER’s emphasis on “effective pollen flow”, it tends to yield shorter average pollination distances. The two approaches are complementary, but suited to different sampling designs and questions. Here, we attempt to reconcile sometimes-divergent findings while also discussing emerging findings on pollen movement across complex landscapes.
Over-exploitation and fragmentation are serious problems for tropical forests. Most sustainable forest management practices avoid clear-cuts and apply selective logging systems focused on a few commercial species. We applied a simulation model to estimate the impact of such selective logging scenarios on the genetic diversity and demography of four tropical tree species from French Guiana. The simulations used data on genetic and demographic composition, growth, phenology and pollen and seed dispersal obtained for Dicorynia guianensis, Sextonia rubra, Symphonia globulifera and Vouacapoua americana at the experimental site in Paracou. Whereas Symphonia globulifera serves as a model for a species with low logging pressure, the other three species represent the most exploited tree species in French Guiana. In simulations with moderate logging, typical for French Guiana, with large cutting diameter (>60 cm diameter) and long cutting cycles (65 years), the two species V. americana and Sextonia rubra were not able to recover their initial stock at the end of the rotation period, with a large decrease in the number of individuals and in basal area. Under a more intensive logging system (cutting diameter >45 cm diameter, cutting cycles of 30 years) that is common practice in the Brazilian Amazon, only Symphonia globulifera showed no negative impact. Generally, the differences between the genetic parameters in the control scenarios without logging and the logging scenarios were surprisingly small. The main reasons for this were the overlapping of generations and the effective dispersal ability of gene vectors in all species, which guarantee relative homogeneity of the genetic structure in different age classes. Nevertheless, decreasing the population size by logging reduced the number of genotypes and caused higher genetic distances between the original population and the population at the end of the logging cycles. Sensitivity analysis showed that genetic changes in the logging scenarios were principally determined by the growth, densities and cutting diameter of each species, and only to a very small extent by the reproductive system including factors such as pollen and seed dispersal and flowering phenology.
The extent of clonal reproduction may significantly influence the genetic structure and reproductive ability of wild cherry (Prunus avium L.) populations. In this study we used simple sequence repeat (SSR) variation to examine the relative frequency and distribution of vegetatively derived wild cherry in two ancient woodlands subject to contrasting management regimes. The probability of identical genotypes arising through sexual reproduction was determined to be negligible, both statistically and through screening a large population of known full-siblings. Only 246 genotypes were identified in the 551 trees examined from the natural populations. Thus, asexual recruitment accounted for a significant proportion of trees. Forty-five genets with multiple clonal trees (clonal groups) were identified. Clonal trees accounted for approximately 48% and 65% of all trees in the managed and unmanaged sites, respectively. Wild cherry trees were distributed in an aggregated manner, but to a stronger degree in the unmanaged woodland which was characterised by a disrupted canopy layer created by storm damage. However, clonal groups were generally non-exclusive in their distribution and displayed a ‘guerrilla’ strategy where further single and multi-ramet genotypes commonly shared the territory of the dominant clone. The clonal groups at the managed site were more exclusive than those in the unmanaged site. Evidence of somatic mutation occurring within clonal groups (i.e. where neighbouring trees matched at all except one locus and the disparity between groups was restricted to a single SSR repeat unit) was also observed, adding further complexity to the clonal structure of wild cherry. Natural disturbance and woodland management appear to influence clonal structure at this study site. Clonal genets in the unmanaged site contained significantly higher numbers of significantly smaller ramets and, on average, covered less than half the area of clonal groups at the managed site. Recruitment, both asexual and sexual, was also markedly higher at the unmanaged site and disproportionately high in years following major winter storms and attendant disturbance of the canopy. Whilst high levels of clonality were observed in both sites it is likely that self-incompatibility and the ‘guerrilla’ strategy of clonal growth adopted by wild cherry enable relatively high levels of genetic diversity to be maintained. Our study suggests that a policy of non-management, especially following winter storms, may help maintain genetic diversity through increased levels of both sexual and asexual recruitment in wild cherry.
As conservation genetics is integrated into multipurpose forest management, questions regarding the genetic effects of silviculture arise. Careful harvesting regimes, using natural regeneration, could preserve genetic resources within commercially important species, both in reserves and in logged areas. We investigated the effects of two natural regeneration methods, shelterwood and group selection cutting, on subsequent pollen movement and mating system in four native stands of monospecific Scots pine (Pinus sylvestris L.) in the Guadarrama Chain of central Spain. Using TwoGener analysis, we estimated an average pollination distance of 17–22 m and a relatively large effective number of pollen donors (Nep>70). We found a non-significant trend toward increasing pollination distance and larger effective number of pollen donors, subsequent to cutting. Considering the high conspecific density of the stands we studied (80–315 trees/ha), pollen dispersal estimates seem consistent with values from other studies, using other methods. Mating system analysis, using the MLTR mixed-mating model, showed high outcrossing rates for all four stands (tm=0.93–0.99), but failed to show significant effects of stand thinning, although slight increases of the outcrossing rate and the apparent rate of consanguineous mating (tm–ts) occurred, subsequent to cutting. Results suggest that the pollination system of Scots pine is resilient enough to preclude a negative impact of natural regeneration cutting. From the pollination point of view, normal Scots pine silvicultural systems seem compatible with genetic conservation purposes in central Spain.
Forest logging reduces population density and increases the distance between co-specifics and so can cause the loss of alleles, and affect the genetic diversity, spatial genetic structure (SGS), mating system, and pollen flow of the population. These factors were studied in the tropical tree species Bagassa guianensis Aubl. occurring in a low-density population in the Brazilian Amazon forest. Genetic diversity was compared among offspring, juveniles and adult trees, before and after selective logging. Non-significant differences were observed between these samples. The harvest of 61% of the adult trees caused the loss of three alleles in the reproductive population. However, these alleles were present in juveniles and offspring and so were not lost from the population. SGS was detected up to 300 m before logging in the overall and adult populations. After logging, significant SGS was not observed. Deviations from random matings were evident throughout biparental inbreeding (, P < 0.05), correlated mating (, P < 0.05), and differentiation in pollen gene pool (, P < 0.05). The effective number of pollen donors was estimated as 5–7 trees. The distance of pollen gene dispersal was estimated as 308–961 m, depending on the dispersal model used (normal and exponential) and assumed population density. The estimated neighbourhood pollination area (Aep) ranges from 81 to 812 ha, depending also on the assumed population density. Reproduction by obligatory outcrossing, pollen immigration from trees outside of the plot, the long-pollen dispersal distance, and large Aep suggested that the species can be resilient to the impacts of logging.
Comparative analyses of spatial genetic structure (SGS) among species, populations, or cohorts give insight into the genetic consequences of seed dispersal in plants. We analysed SGS of a weedy tree in populations with known and unknown recruitment histories to first establish patterns in populations with single vs. multiple founders, and then to infer possible recruitment scenarios in populations with unknown histories. We analysed SGS in six populations of the colonizing tree Albizia julibrissin Durazz. (Fabaceae) in Athens, Georgia. Study sites included two large populations with multiple, known founders, two small populations with a single, known founder, and two large populations with unknown recruitment histories. Eleven allozyme loci were used to genotype 1385 individuals. Insights about the effects of colonization history from the SGS analyses were obtained from correlograms and Sp statistics. Distinct differences in patterns of SGS were identified between populations with multiple founders vs. a single founder. We observed significant, positive SGS, which decayed with increasing distance in the populations with multiple colonists, but little to no SGS in populations founded by one colonist. Because relatedness among individuals is estimated relative to a local reference population, which usually consists of those individuals sampled in the study population, SGS in populations with high background relatedness, such as those with a single founder, may be obscured. We performed additional analyses using a regional reference population and, in populations with a single founder, detected significant, positive SGS at all distances, indicating that these populations consist of highly related descendants and receive little seed immigration. Subsequent analyses of SGS in size cohorts in the four large study populations showed significant SGS in both juveniles and adults, probably because of a relative lack of intraspecific demographic thinning. SGS in populations of this colonizing tree is pronounced and persistent and is determined by the number and relatedness of founding individuals and adjacent seed sources. Patterns of SGS in populations with known histories may be used to indirectly infer possible colonization scenarios for populations where it is unknown.
Les systèmes de reproduction jouent un rôle fondamental dans la structuration spatio-temporelle de la diversité génétique des espèces. Cette thèse, portant sur l'étude de trois populations de merisiers, a pour but de mieux comprendre les implications évolutives d'un système de reproduction mixte chez les plantes combinant à la fois une propagation asexuée et une reproduction sexuée contrôlée par un système d'auto-incompatibilité gamétophytique (GSI).Nous avons étudié les influences de la propagation asexuée et du GSI sur (1) la structuration diversité génétique intra et inter populations et sur (2) l'efficacité de sa transmission d'une génération à l'autre.Confrontant des modèles et concepts théoriques aux réalités biologiques, nos résultats démontrent à la fois un effet de l'asexualité et du GSI sur l'évolution de la diversité génétique de notre espèce. Ces effets sont plus complexes voire contraires à ce que prédisent les modèles ou les concepts actuellement admis.
The effective population size is required to predict the rate of inbreeding and loss of genetic variation in wildlife. Since only census population size is normally available, it is critical to know the ratio of effective to actual population size (Ne/N). Published estimates of Ne/N (192 from 102 species) were analysed to identify major variables affecting the ratio, and to obtain a comprehensive estimate of the ratio with all relevant variables included. The five most important variables explaining variation among estimates, in order of importance, were fluctuation in population size, variance in family size, form of N used (adults υ. breeders υ. total size), taxonomic group and unequal sex-ratio. There were no significant effects on the ratio of high υ. low fecundity, demographic υ. genetic methods of estimation, or of overlapping υ. non-overlapping generations when the same variables were included in estimates. Comprehensive estimates of Ne/N (that included the effects of fluctuation in population size, variance in family size and unequal sex-ratio) averaged only 0·10–0·11. Wildlife populations have much smaller effective population sizes than previously recognized.
Small populations of self-incompatible plants are assumed to be threatened by a limitation of compatible mating partners due to low genetic diversity at the self-incompatibility (S) locus. In contrast, we show by using a PCR-RFLP approach for S-genotype identification that 15 small populations (N = 8-88) of the rare wild pear (Pyrus pyraster) displayed no mate limitation. S-allele diversity within populations was high (N = 9-21) as was mate availability (92.9-100%). Although population size and S-allele diversity were strongly related, no relationship was found between population size and mate availability, gene diversity (He), or fixation index (F(IS)), based on five neutral microsatellite loci. As we determined the principal mate availability within populations based on the S-genotypes observed, the realized mate availability under natural conditions may differ from our estimates, for example, due to spatially limited pollen dispersal. We therefore urge studies on self-incompatible plants to proceed from the simple assessment of principal mate availability to the determination of realized mate availability in natural populations.
The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.
Spatial autocorrelation analyses of 12 allozyme loci were used to compare genetic structure within populations of two varieties of Pinus clausa. P. clausa var. immuginata populations tend to be uneven-aged, with continuous recruitment in small gaps created by wind damage, whereas P. clausa var. clausa populations are more even-aged, with recruitment postdating periodic canopy fires. Three var. immuginata populations and three matched pairs of var. clausa populations, including both a mature and a nearby recently burned population, were examined. Aggregation of multilocus genotypes at small distances was evident in all young var. clausa populations. Little inbreeding was apparent among juveniles or adults in these populations; their genetic structure is likely to have resulted from limited seed dispersal. Genotypes were not significantly spatially structured in nearby matched mature populations. Genetic structure was less evident in var. immuginata populations. Aggregated genotypes were only apparent in the population where patches included juveniles of similar ages; dense juvenile clumps in the other two var. immuginata populations comprised a variety of ages. Interannual variability in allele frequencies of surviving seedlings may account for the absence of genetic structure in these populations.
The fine-scale spatial genetic structure of eight tropical tree species (Chrysophyllum sanguinolentum, Carapa procera, Dicorynia guianensis, Eperua grandiflora, Moronobea coccinea, Symphonia globulifera, Virola michelii, Vouacapoua americana) was studied in populations that were part of a silvicultural trial in French Guiana. The species analysed have different spatial distribution, sexual system, pollen and seed dispersal agents, flowering phenology and environmental demands. The spatial position of trees and a RAPD data set for each species were combined using a multivariate genetic distance method to estimate spatial genetic structure. A significant spatial genetic structure was found for four of the eight species. In contrast to most observations in temperate forests, where spatial structure is not usually detected at distances greater than 50 m, significant genetic structure was found at distances up to 300 m. The relationships between spatial genetic structure and life history characteristics are discussed.
Camellia japonica L. (Theaceae), an insect- and bird-pollinated, broad-leaved evergreen tree, is widely distributed in Japan and the southern Korean peninsula. The species has a relatively even age distribution within populations, which may influence the spatial genetic structure of different age classes relative to species with typical L-shaped age distributions. To determine whether the internal spatial genetic structure found in seedlings and young individuals carries over into adults, we used allozyme loci, F-statistics, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among seven age classes in a population (60-m x 100-m area) in southern Korea. In seedlings, weak but significant positive values of Moran's I-statistics and coancestry measures were found for distances less than 14 m, which is consistent with a mechanism of limited seed dispersal combined with overlapping seed shadows. This spatial structure, however, dissipates in older age classes, and in adults genetic variation has an essentially random spatial distribution. Morisita's index of dispersion of individuals in each age class showed that seedlings and juveniles are more highly clustered than are older individuals. These results suggest that self-thinning changes the spatial relationships of individuals, and thus genotypes. A multilocus estimate of FST (0.008) shows a small but statistically significant difference in allele frequencies among age classes. In summary, intrapopulation genetic structure within and among age classes of C. japonica was significant but weak. Despite presumably limited seed dispersal, weak spatial genetic structure in juveniles suggests overlapping seed shadows followed by self-thinning during recruitment. The present study also demonstrates that studies of spatial genetic structure focusing on limited numbers of generations may not be sufficient to reveal the entire picture of genetic structure in populations with overlapping generations.
A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy-Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full-sibs, and performs better than a previously developed estimator. When comparing marker-based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co-dominant markers (microsatellites) in studying microgeographic isolation-by-distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.
A survey of Australian cherry orchards identified the cherry cultivars Sunburst, Summit, Merchant, Sam, Sylvia, Tieton, Kordia, Regina, Empress, Nordwunder and Ulster as having low fruit-set associated with poor pollination. Unique orchard sites across Australia where low fruit-set was not a problem for these cultivars were located, and pollen gene-flow-analysis conducted using 6-PGD, GOT, G6PD, GPI, IDH, FDP and SKDH isozyme markers. Pollenisers for the above-mentioned cultivars were determined and Stella was a polleniser for eight of them. Stella's predominance was linked to it reaching full bloom before the other cultivars; anther dehiscence occurs sometime after flowers open, as such newly opened flowers; the most-fertile stage was mainly exposed to Stella pollen. Sunburst a self-compatible cultivar showed no evidence of self-fertilisation. The majority of pollenisers were found to be within 20 m of the tree under examination. Isozyme profiles for 22 cultivars not previously analysed are also presented.
PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S(1) to S(6) S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S(13), these also amplified S(7) to S(14) and an allele previously referred to as S(x), which we now label S(16). The genomic PCR products were cloned and sequenced. The partial sequence of S(11) matched that of S(7) and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S(7) to S(16), so that allele-specific primers are now available for all 13 S alleles of cherry (S(8), S(11) and S(15) are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S(3) S(16)), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S(6) S(12)), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S(3) S(3)', S(4)' S(6), S(4)' S(9) and S(4)' S(13), were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.
Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.
Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an 'Sp' statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.
ABSTRACT The self-incompatibility (S) genotypes of a collection of 65 Belgian accessions of wild cherry, selected within two populations and planted in a seed orchard, were determined using polymerase chain reaction (PCR) methods. Initially, DNA extracts were amplified with consensus primers that amplify across the second intron of the S-ribonuclease gene which shows considerable length polymorphism. The provisional genotypes deduced were checked with the appropriate allele-specific primers for the known alleles S(1) to S(16). Putative new alleles were subjected to PCR with consensus primers amplifying across the first intron. Six new alleles, S(17) to S(22), were thus indicated on the basis of the estimated lengths of the first and second intron PCR products. Examples of these alleles were partially sequenced and were indeed mutually distinct and different from the known alleles. The incompatibility genotypes of all 65 accessions were determined and one triploid individual was found. Seventeen alleles were detected in all. Allele frequencies differed between samples and the expected total number of alleles in the underlying populations was estimated. The wild cherry populations differed significantly with respect to allelic frequencies from sweet cherry cultivars; alleles S(4) and S(5), which are moderately frequent in sweet cherry, were absent from the wild cherry accessions. The knowledge of the S genotypes will be useful for studying the gene flow within the seed orchard and these approaches should also be informative in wild populations.