Genetic differences within natural and planted stands of <Emphasis Type="Italic">Quercus petraea</Emphasis>

Five sessile oak [Quercus petraea (Matt.) Liebl.] stands from the Czech Republic were studied to learn about the impact of different types of forest management regimes on the genetic differences among tree populations and on population structures. One population had not been markedly affected by human activity, two populations represented unplanted stands that were extensively managed for a long period of time using the coppice system, and two populations were planted stands. Approximately 100 trees from each stand were mapped and subsequently genotyped using 10 nuclear microsatellite loci. We determined the spatial genetic structure of each population and the genetic differentiation among the populations. We found that: (i) the populations were genetically differentiated, but the differences between the unplanted and planted stands were not markedly significant; (ii) the genetic differentiation among the populations depended on the geographical distribution of the populations; (iii) within unplanted stands, a strong spatial genetic structure was seen; and (iv) within planted stands, no spatial genetic structure was observed. Our findings implies that the analysis of spatial genetic structure of the sessile oak forest stand can help reveal and determine its origin.     

Adaptive responses for seed and leaf phenology in natural populations of sessile oak along an altitudinal gradient

We assessed the adaptive potential of seed and leaf phenology in 10 natural populations of sessile oak (Quercus petraea) sampled along two altitudinal transects using common garden experiments. Population differentiation for both phenological traits was observed with high-altitude populations germinating and flushing later than low altitude ones. However, high genetic variation and heritability values were also maintained within populations, despite slightly decreasing for dates of leaf unfolding with increasing altitude. We suggest that biotic and abiotic fluctuating selection pressures within populations and high gene flow are the main mechanisms maintaining high genetic variation for these fitness related traits. Moreover, changes in selection intensity and/or selection pressures along the altitudinal gradient can explain the reduction in genetic variation observed for leaf phenology. We anticipate that the maintenance of high genetic variation will be a valuable resource for future adaptation of sessile oak populations undergoing an upslope shift caused by climate change.     

Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late‐successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.     

Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains

Aim To understand global patterns of genetic variation in plant species on mountains and to consider the significance of mountains for the genetic structure and evolution of plant species. Location Global. Methods We review published studies. Results Genetic diversity within populations can vary along altitudinal gradients in one of four patterns. Eleven of 42 cited studies (26% of the total) found that populations at intermediate altitudes have greater diversity than populations at lower and higher altitudes. This is because the geographically central populations are under optimal environmental conditions, whereas the peripheral populations are in suboptimal situations. The second pattern, indicating that higher populations have less diversity than lower populations, was found in eight studies (19%). The third pattern, indicating that lower populations have lower diversity than higher populations, was found in 10 studies (24%). In 12 studies (29%), the intrapopulation genetic variation was found to be unaffected by altitude. Evidence of altitudinal differentiation was found in more than half of these studies, based on measurements of a range of variables including genome size, number of chromosomes or a range of loci using molecular markers. Furthermore, great variation has been found in phenotypes among populations at different altitudes in situ and in common garden experiments, even in cases where there was no associated variation in molecular composition. Mountains can be genetic barriers for species that are distributed at low elevations, but they can also provide pathways for species that occupy high‐elevation habitats. [Correction added after publication 9 October 2007: ‘less diversity’ changed to ‘greater diversity’ in the second sentence of the Results section of the Abstract] Main conclusions Genetic diversity within populations can vary along altitudinal gradients as a result of several factors. The results highlight the importance of phenotypic examinations in detecting altitudinal differences. The influence of mountain ridges on genetic differentiation varies depending, inter alia, on the elevation at which the species occurs. Based on these findings, zoning by altitudes or ridges would be helpful for the conservation of tree populations with the onset of global warming.     

Genetic variation of oaks (<Emphasis Type="Italic">Quercus</Emphasis> spp.) in Switzerland. 3. Lack of impact of postglacial recolonization history on nuclear gene loci

Quercus petraea, Quercus pubescens and Quercus robur are closely related and interfertile white oaks native to Switzerland. The three species are known to share identical cpDNA haplotypes, which are indicative of the postglacial recolonization history of populations. Only two haplotypes are common in Switzerland. We compared variation of cpDNA and of isozymes in 28 oak populations from Switzerland in order to assess the impact of the postglacial population history on current genetic structures of nuclear controlled isozyme gene loci. Species delineation was based on Principal Component Analysis of leaf morphological traits. The species status of populations was reflected at isozyme gene loci, but differentiation between populations with different cpDNA haplotypes and hence different recolonization history was very low at enzyme gene loci for all species. Thus, glacial and postglacial population history was not reflected at nuclear gene loci on the temporal and spatial scale covered by the present study. Extensive gene flow through pollen among populations is likely to have blurred a previously existing genetic differentiation at biparentally inherited gene loci that possibly evolved in the different glacial refugia of the above mentioned cpDNA haplotypes.     

The Balearic Islands: a reservoir of cpDNA genetic variation for evergreen oaks

Aim To analyse the role of the Balearic Islands as a refuge area for evergreen Quercus (cork oak: Quercus suber L., holm oak: Q. ilex L., kermes oak: Q. coccifera L.), by using molecular, historical and palaeobotanical data. Location The Western Mediterranean Basin (Balearic Islands, eastern Iberia, Provence, Sardinia, Corsica, Sicily, Malta, Italy, Northern Africa). Methods We sampled 108 populations and used the PCR‐RFLP technique with five universal cpDNA primers to define haplotypes in the sampled populations. Diversity, differentiation parameters and spatial analysis of the populations, using a spatial version of amova , were linked to the geological history of the Western Mediterranean Basin in order to explain the present spatial pattern of the evergreen Quercus populations in the Balearics. Results Evergreen Quercus cpDNA shows a complex structure, with remnants of ancient diversity in the Balearics. Balearic populations of holm oak are related to Iberian populations, while for cork and kermes oaks, we found both Tyrrhenian and Iberian haplotypes. Main conclusions The complex spatial patterns of cpDNA in Balearic evergreen Quercus appears explicable in terms of a combination of physical (vicariance and long distance dispersal) and biological (introgressive hybridization) factors. The Balearics constitute a glacial refuge area and a reservoir of genetic variation with traces of ancient diversity from Messinian–Pliocene stages.     

Genetic diversity analysis of Rhododendron aureum Georgi (Ericaceae) located on Changbai Mountain using ISSR and RAPD markers

Rhododendron aureum Georgi (Ericaceae) is a perennial alpine shrub endemic to Changbai Mountain in China. We used ISSR and RAPD markers to describe the diversity and genetic structure within and among four natural populations located at different altitudes. DNA from 66 individuals was amplified with ten ISSR markers and seven RAPD markers. High genetic diversity was observed by these two techniques at the species level. The genetic diversity of populations increased with altitudinal gradients from low to high. The coefficient of gene differentiation (G_ST 0.3652 in ISSR and 0.2511 in RAPD) and AMOVA analysis revealed that most genetic diversity was distributed within populations (61.96% in ISSR and 70.23% in RAPD). The estimate of gene flow based on G_ST was 0.8690 in ISSR and 1.4910 in RAPD. The UPGMA clustering results using ISSR and RAPD showed that all individuals from the same altitude were gathered together, and the two populations (TYD2a and YHLa) from middle altitudes always clustered together. Compared with populations from different altitudes, similar genetic diversity and low genetic differentiation were obtained from populations at the same altitudes, as revealed by ISSR markers. In addition to the reproductive strategy of R. aureum, these data highlight that local environmental conditions may play an important role in shaping the diversity and genetic structure of this species.     

A set of primers for the amplification of chloroplast microsatellites in Quercus

The increase in demand for the certification of oak seed lots, as well as control of the geographical origin of oak wood, has led us to develop powerful genetic markers permitting us to discriminate among provenance regions. With the aim of detecting new chloroplast variants, we have identified 17 potential cpSSRs motifs from available oak sequences and tested their variability among French oak populations. Six loci were polymorphic at the intraspecific level in Quercus petraea and Q. robur. Moreover, conservation of the primer pairs was checked on a set of 21 forest tree species and they were all shown to work well on several Quercus species, and even within Fagacaea.     

MATING SYSTEM AND ASYMMETRIC HYBRIDIZATION IN A MIXED STAND OF EUROPEAN OAKS

The sessile (Quercus petraea [Matt.] Liebl.) and pedunculate (Quercus robur L.) oaks are two closely related species having a wide sympatric distribution over Europe. Under natural conditions, they frequently form mixed forests, where hybridization is suspected to occur. In this paper, two different approaches have been applied to the study of the mating system and the interspecific gene flow in a mixed stand formed by the two species. The mating systems of both species have been studied separately by means of the mixed-mating model. The relative contribution of the parental species to the progenies have been estimated with two different methods. The first uses the admixture model. The second is an extension of the mixed-mating model and subdivides the outcrossing rate into intra- and interspecific components. The two species were almost completely outcrossing. This high level of outcrossing and interspecific gene flow could play an important role in the maintenance of the genetic diversity in these long-lived forest tree species. The contribution of the sessile oak to the pedunculate oak progenies varied from 17% to 48%. In contrast, ovules of sessile oak trees appear to be preferentially fertilized by other extreme sessile genotypes. We suggest that interspecific and directional gene flow was responsible for such patterns. Pedunculate oak is considered as a pioneer species and is progressively replaced by sessile oak. Our present findings add a further genetic component to this succession scheme, suggesting that unidirectional gene flow reinforces succession between the two species.     

Low genetic differentiation among populations ofArabis serrata (Brassicaceae) along an altitudinal gradient

We investigated the extent of genetic differentiation among populations of fujihatazao,Arabis serrata along an altitudinal gradient at Mt. Fuji in Shizuoka Prefecture. This species is a perennial plant, widely distributed in Japan forming small isolated populations. However, at Mt. Fuji, this species constitutes a large population distributed from 1440 to 2400 m altitude. A total of 411 individuals were sampled from ten subpopulations. Eighteen loci were detected on eleven enzyme systems. Eleven loci were monomorphic and seven loci were polymorphic with a mean of 2.11 alleles per loci. Nei's genetic distance (mean 0.01) and genetic identity (mean 0.968) were very similar among populations indicating a low genetic differentiation. The total genetic diversity (H _T ) estimated for the polymorphic loci was, in average, 0.396. The mean gene differentiation (G_ST=0.091) was very low. Gene frequency of seven polymorphic loci was analyzed by spatial autocorrelation methods based on Moran's indexes. Only Pgi-3 exhibited a significant negative autocorrelation (−0.160;P<0.05); other loci values ranged from −0.134 to 0.027. Gene flow estimated by indirect methods varied between genes but most of the values were high (meanNm=20.8) suggesting that subpopulations at different altitudes are probably connected. Despite plants at different altitudes present different ecological traits (e.g., differences in phenology, growth and reproductive traits), subpopulations ofA. serrata are still low differentiated, at least for the loci studied. This may be explained by the recent origin of some habitats (e.g., second crater and surrounded areas) in this locality.     

Patterns of Genetic Variation across Altitude in Three Plant Species of Semi-Dry Grasslands

Background

Environmental gradients caused by altitudinal gradients may affect genetic variation within and among plant populations and inbreeding within populations. Populations in the upper range periphery of a species may be important source populations for range shifts to higher altitude in response to climate change. In this study we investigate patterns of population genetic variation at upper peripheral and lower more central altitudes in three common plant species of semi-dry grasslands in montane landscapes.

Methodology/Principal Findings

In Briza media, Trifolium montanum and Ranunculus bulbosus genetic diversity, inbreeding and genetic relatedness of individuals within populations and genetic differentiation among populations was characterized using AFLP markers. Populations were sampled in the Swiss Alps at 1800 (upper periphery of the study organisms) and at 1200 m a.s.l. Genetic diversity was not affected by altitude and only in B. media inbreeding was greater at higher altitudes. Genetic differentiation was slightly greater among populations at higher altitudes in B. media and individuals within populations were more related to each other compared to individuals in lower altitude populations. A similar but less strong pattern of differentiation and relatedness was observed in T. montanum, while in R. bulbosus there was no effect of altitude. Estimations of population size and isolation of populations were similar, both at higher and lower altitudes.

Conclusions/Significance

Our results suggest that altitude does not affect genetic diversity in the grassland species under study. Genetic differentiation of populations increased only slightly at higher elevation, probably due to extensive (historic) gene flow among altitudes. Potentially pre-adapted genes might therefore spread easily across altitudes. Our study indicates that populations at the upper periphery are not genetically depauperate or isolated and thus may be important source populations for migration under climate change.     

Storage-protein variation in wild emmer (Triticum turgidum ssp.dicoccoides) from Jordan and Turkey.

Genetic diversity in the seed storage-proteins encoded at theGlu-A1,Glu-B1 andGli-B1/Glu-B3 loci was studied electrophoretically in 315 individuals belonging to nine populations ofT. dicoccoides from Jordan and three from Turkey. The inter- and intra-population distribution of seed storage-protein alleles at the considered loci and its link with geographical factors were investigated. Population differentiation in seed storage-proteins was in some cases very high with very weak correlations with geographic distance. Greater gene differentiation was found within and between populations which were geographically very close in Jordan than between those from Jordan and Turkey. However the distribution of alleles appeared to be non random. Samples collected from populations at locations over 900 m above sea level were less polymorphic than those collected at lower altitudes (500–700 m), whereas the relative genetic differentiation between populations was greater between those collected at higher altitudes. Seed storage-protein differentiation was significantly correlated with the altitude of the collecting sites. Although it is difficult to point out the selective pressure of altitude per se, altitude can reflect an integration of several environmental parameters. The possible adaptive value of seed storage-proteins is discussed.     

Genetic evaluation of eri silkworm <Emphasis Type="Italic">Samia cynthia ricini</Emphasis>: ISSR loci specific to high and low altitude regimes and quantitative attributes

Genetic structure of populations is under constant pressure from varying geographical conditions that induce phenotypic plasticity in insects. Spatial distribution of 15 populations of Indian eri silkworm, Samia cynthia ricini originated at various altitudes of sub Himalayas based on Euclidean distance realized from yield attributes showed two population clusters irrespective of their place of origin and altitude. However, DNA amplification profile by inter SSR (ISSR) markers showed genetic variations among the populations depend on low and high altitudes. One ISSR locus each specific to high and low altitude population was identified. The locus from high altitude showed deviation from Hardy-Weinberg equilibrium but that from low altitude was in neutrality suggests that the high altitude loci could be under pressure from the altitudinal variations. In association with different yield traits, 18 loci were identified. Of which, three markers showed association with more than one trait indicative of pleiotropic influence. Stepwise addition of markers enhanced the correlation between markers and the associated trait pointed to polygenic influence. Association of markers with altitude and yield traits suggests an imperative relation of rare genetic loci with gene-environment interaction and phenotypic variability in S. c. ricini.     

Characterisation and natural variation of a dehydrin gene in Quercus petraea (Matt.) Liebl

For the first time in sessile oak [Quercus petraea (Matt.) Liebl.], the isolation and characterisation of a full-length dehydrin gene and its promoter region, as well as its allelic variation in natural populations, is reported. Dehydrins (Dhn) are stress-related genes important for the survival of perennial plants in a seasonal climate. A full-length dehydrin gene (Dhn3) was characterised at the nucleotide level and the protein structure was modelled. Additionally, the allelic variation was analysed in five natural populations of Quercus petraea (Matt.) Liebl. sampled along an altitudinal gradient in the French Pyrenees. The analysed sequences contain typical domains of the K(n) class of dehydrins in the coding region. Also, the 5'untranslated region (promoter) of the gene was amplified, which shows typical motifs essential for drought- and cold-responsive gene expression. Single nucleotide substitutions and indels (insertions/deletions) within the coding region determine large biochemical differences at the protein level. However, only low levels of genetic differentiation between populations from different altitudes were detectable.     

Hybridisation and colonisation dynamics in European oaks

Summary

Extensive hybridisation between the two sympatric species Quercus petraea and Q.robur is suggested by the near lack of genetic differentiation between the two species and supported by controlled crosses and mating system analysis in mixed stands. Further ecological and genetic evidence suggest that hybridisation does not impede the ecological specialisation of the two species, raising the issue of its evolutionary significance in oaks. Preferential unidirectional hybridization (pollen Q. petraea to ovule Q. robur) has been shown in various mixed stands and facilitates the introduction of sessile oak in existing pedunculate stands. If this unidirectional trend is reinforced in later backcrosses, then hybridisation leads to the dispersal of Q. petraea in existing stands of Q. robur. Hybridisation can therefore be seen as a ‘pollen-mediated’ dispersal mechanism, and has most likely contributed to the rapid migration of Q. petraea in Europe. Given the extant distribution of the species in Europe, migration through pollen swamping should be seen at the edges of the natural distribution of Q. petraea where the demographic imbalance of the two species will reinforce backcrosses.     

Genetic variability of fragmented stands of pedunculate oak (Quercus robur) in Finland

The genetic structure of 33 natural Quercus robur stands in Finland was studied using 13 allozyme loci to analyze the effects of fragmentation in a wind-pollinated tree species. The present fragmented and discontinuous distribution of oak is a result of both short-term human impact and long-term climatic and geological change, including post-glacial land uplift. In accordance with general expectations, genetic diversity in small populations was lower than that in large populations, and differentiation among small populations was higher than that among large populations. Heterozygote deficiency was more pronounced in large populations, which is proposed to be a Wahlund effect created by either spatial sub-structuring or the existence of synchronized flowering lineages. Also genetic differentiation was higher and diversity lower in Finland than the estimates reported for Central Europe. There were differences in the genetic structure on sites of different geological age. We suggest that on most geologically old sites drift has a prominent effect whereas on younger sites also founder effects may be important.     

Morphological and molecular diversity among Italian populations of Quercus petraea (Fagaceae)

Quercus petraea (sessile oak) has a scattered distribution in southern and central Italy. The objective of this work was to evaluate the level and distribution of diversity in five Italian populations of Q. petraea by using morphological markers and hypervariable molecular markers such as microsatellites. Forty-eight morphological traits and six nuclear and three plastid loci were scored for each population. Evidence for differentiation in both sets of traits was found, but patterns of differentiation of morphological traits did not coincide with microsatellite differentiation. Morphological variation was correlated with ecological conditions at the site of origin. Analysis of molecular variance revealed significant genetic variation among populations (P < 0.001), both at the nuclear and plastid levels. There was a slight, but significant, correlation between nuclear genetic distance and geographic distance. The relatively high genetic diversity in the populations analysed indicates that the maintenance of their evolutionary potential is possible if population sizes are maintained or increased. Low levels of haplotype diversity found within the small southernmost population (Piano Costantino) indicates that genetic erosion may increase the extinction risk for this population.     

Contact zone of two different chloroplast lineages and genetic guidelines for seed transfer in Quercus serrata and Quercus crispula

Within their natural distribution ranges, plant species exhibit a genetic structure that has been created by global climate change and natural selection over long periods. This genetic structure needs to be conserved for sustainable use of genetic resources. To conserve local forests with different genetic structures, genetic guidelines for seed and seedling transfer in individual species are necessary. Genetic guidelines have been published for 43 Japanese tree species using population genetic data; however, for practical use, more detailed genetic borders between important genetic lineages should be clarified to inform seed collection and planting. Thus, we investigated in detail the genetic borders between two important Japanese oak species, Quercus serrata and Quercus crispula, in the Chubu region of Japan using chloroplast and nuclear DNA markers, and we discuss the factors that influenced border creation using the results of species distribution modeling (SDM). The chloroplast DNA (cpDNA) haplotype was clearly different within the Chubu region of Japan but the difference in nuclear DNA between northern and southern haplotype populations was very small, both in Q. serrata and Q. crispula. The results of SDM showed that during the last glacial maximum (LGM) Q. serrata was distributed mostly along the coastline but Q. crispula was distributed not only along the coast but also in mountainous areas further inland. The cpDNA genetic borders of these two oak species are complex and seem to have been influenced by topography and their distribution during the LGM. We propose and discuss genetic guidelines for these two oak species based on the results of this study.     

Allozyme variation in cork oak (Quercus suber L.): the role of phylogeography and genetic introgression by other Mediterranean oak species and human activities

 Genetic variation in the cork oak (Quercus suber L.) was investigated using 11 loci from seven enzyme systems in 40 populations sampled over the entire distribution of this species in the western Mediterranean Basin. Mean heterozygosity values over the polymorphic loci (Ho=0.283), the percentage of polymorphic populations (M=0.76), and the total genetic diversity (Ht=0.31) from which 11% was accounted for among-population variation, are among the highest recorded in oak species. In contrast to previous results in holm oak (Q. ilex L.), another evergreen species in the same area, cork oak possessed a smaller allele pool and a lower average number of alleles per locus and per population (A=2.0). More particularly, very few low-frequency alleles were observed in cork oak except for eight populations in which allozyme polymorphism at locus Pgi 1, diagnostic between both species, indicates that these low-frequency alleles are introgressed from holm oak. On the basis of the genetic distance estimated from allozyme frequencies, 32 of the 40 cork oak populations studied were classified into two very distinct sets which also corresponded to distinct geographic areas. One set gathered together the 18 populations from the Iberian peninsula and two adjacent areas in France, i.e. the centre of origin of cork oak, according to paleobotanical data. This set was characterized by a larger allele pool, a higher within-population genetic diversity and a lower differentiation between populations than was observed in the other set, which comprised the populations from North Africa, Sicily, Sardinia, Corsica, continental Italy and the region of Provence (southeastern France). In these more southern and eastern disjunct areas, cork oak migration from Iberia may have occurred at different periods since the end of the Tertiary. The possible effect of human activity on cork oak genetic structure, i.e. the selection of good-quality cork, acorn over-use for animal food, and even human nutrition, is discussed. Received: 3 March 1998 / Accepted: 19 March 1998     

Genetic structure along an altitudinal gradient in Lippia origanoides,a promising aromatic plant species restricted to semiarid areas in northern South America

The genetic diversity and population structure of Lippia origanoides, a species of the Verbenaceae family that shows promise as a crop plant, was investigated along an altitudinal gradient in the basin of the Chicamocha River in northeastern Colombia. The economic importance of the species, quality of its essential oils, and the fact that it is restricted to some few semiarid areas in northern South America may put the species at risk in a scenario of uncontrolled harvest of natural populations. Lippia origanoides was sampled along an altitudinal gradient from 365 to 2595 m.a.s.l. throughout Chicamocha River Canyon, a semiarid area in northeastern Colombia. Genetic diversity was assessed by means of AFLP markers. The number of AFLP loci (355) and the number of individuals sampled (173) were sufficient to reliably identify four populations at contrasting altitudes (F_ST = 0.18, P‐value < 0.0000), two populations in the lower basin, one population in the medium basin, and one population in the upper basin, with a low level of admixture between them. In average, genetic diversity within populations was relatively high (Ht = 0.32; I = 0.48); nevertheless, diversity was significantly reduced at higher altitude, a pattern that may be consistent with a scenario of range expansion toward higher elevations in an environment with more extreme conditions. The differences in altitude among the basins in the Chicamocha River seem to be relevant in determining the genetic structure of this species.