Results on quantitative trait loci for flushing date in oaks can be transferred to different segregating progenies

Flushing date (bud burst) is one of the most important traits for the adaptation to different environments and climates in the temperate zone. Because of their wide geographic distribution, Quercus robur L. and Q. petraea (Matt.) Liebl. are suitable as model plants to study the genetic basis of bud burst. QTLs (Quantitative Trait Loci) with comparatively large effects have been mapped in a former study in a Q. robur x Q. robur full-sib family (French cross). In the present study, we performed a Bulked Segregant Analysis (BSA) in the F (1) progeny comprising 144 seedlings derived from a cross between a single Q. robur tree as common seed parent and five different pollen donors both from Q. robur and Q. petraea (Q. robur x Q. spp., Diekholzen crosses). In addition, markers linked to two bud burst QTLs with comparably strong effect in the above-mentioned full-sib family (French cross) were tested for their association with bud burst in the Q. robur x Q. spp. (Diekholzen) progeny. Using three microsatellite markers as anchor points, we could map QTLs on linkage group 7 and on linkage group 2, together explaining 16.2 % of the total phenotypic variance (PVE) in 1999 and 38.1 % in 2003. Out of 10 markers that segregated in both mapping progenies, four markers including the two microsatellite markers, showed a significant effect on bud burst in both materials. At microsatellite loci ssrQpZAG1/5 (linkage group 7) and ssrQpZAG119 (linkage group 2) alleles associated with early (allele 166 bp in ssrQpZAG1/5) and late bud burst (allele 57 bp in ssrQpZAG119) in the Q. robur x Q. robur full-sib family (French cross) showed a highly significant association with the same polarity of the effect in the Q. robur x Q. spp. (Diekholzen) progeny. The usefulness of these markers for marker-assisted selection in full-sib and half-sib families is discussed.     

Hybridization and Rorippa austriaca (Brassicaceae) invasion in Germany

Introgressive hybridization between the invasive Rorippa austriaca and the native R. sylvestris in Germany has been studied using chloroplast DNA (trnL intron) and amplified fragment length polymorphism. Three hybrid zones between the invasive and native species were located in the Ruhr Valley (Mülheim) and at the River Main near Würzburg (Randersacker, Winterhausen). In each hybrid zone hybridization was indicated by additivity of region-specific amplified fragment length polymorphism markers proving independent hybridization events. The hybrids were either morphologically intermediate (R. x armoracioides) or were close to R. sylvestris. The trnL intron of R. austriaca is characterized by a species-specific deletion. This diagnostic chloroplast marker of R. austriaca was detected in three individuals of R. sylvestris providing evidence for introgression of the invasive chloroplast into the native species. Bidirectional introgression of R. austriaca markers into R. sylvestris and of R. sylvestris markers into R. austriaca was detected in the amplified fragment length polymorphism analysis. Some of the invasive R. austriaca populations showed high within-population variation. A possible association among introgression, within-population variation and invasion success is discussed. The morphologically intermediate hybrid R. x armoracioides is currently spreading in northern Germany. It forms large populations without its parent species R. austriaca and R. sylvestris. It is concluded that hybridization between invasive R. austriaca and native R. sylvestris may lead to the evolution of a new invasive species R. x armoracioides.     

Presence of triploids among oak species

BACKGROUND AND AIMS: Polyploids, organisms that have multiple sets of chromosomes, are common in certain plant and animal taxa. However, there are only a few reports of intraspecific ploidy variation within the genus Quercus. The aim of the study was to investigate the suspected ploidy level of two oaks that have unusual microsatellite banding patterns. METHODS: Polyploidy was investigated by using microsatellite analysis, stomata length measurements and nuclear DNA content estimation by flow cytometry. KEY RESULTS: Each putative triploid tree has patterns of microsatellite variation unexpected for diploid genomes, with up to three alleles at some loci, significantly longer stomata and 1.5 times more DNA per nucleus compared with diploids. CONCLUSIONS: To our knowledge, this report contains the first evidence for triploidy in Q. petraea and confirmation of this phenomenon in Q. robur. Regardless of the positive or negative aspects of the presence of triploid oaks in forest stands, it is of value to be able to screen for them. This study demonstrates that nuclear microsatellites and estimation of DNA content by flow cytometry can readily be used for this purpose.     

The Description of Clones of Quercus robur L. and Q. petraea (Matt.) Liebl. with Microsatellites and AFLP in an Ancient Woodland

Abstract: In densely populated areas autochthonous Quercus robur L. (pedunculate oak) and Q. petraea (Matt.) Liebl. (sessile oak) (Fagaceae) populations have been maintained as ancient devastated woodlands. The continuous cutting, grazing and resprouting of such woodlands has enabled the development of clonal structures. For conservation purposes, an analysis of the actual number, size and spatial distribution of clones is necessary, especially when there is an interest in genetic variation of the population. This study describes for the first time - based on microsatellite and AFLP™ analysis - clones in an autochthonous mixed Q. robur and Q. petraea population that has been coppiced and grazed for several centuries. Based on six microsatellite loci and 69 polymorphic AFLP markers, only 14 unique genotypes were detected in a plot that consisted of 80 trees. Clones were observed for both Q. robur and Q. petraea. The largest clone diameters were observed for Q. robur, with distances up to 5.8 m. The observed clone sizes may indicate the age of the trees.     

Species distinction in Irish populations of Quercus petraea and Q. robur: morphological versus molecular analyses

BACKGROUND AND AIMS: Populations of oak (Quercus petraea and Q. robur) were investigated using morphological and molecular (AFLP) analyses to assess species distinction. The study aimed to describe species distinction in Irish oak populations and to situate this in a European context. METHODS: Populations were sampled from across the range of the island of Ireland. Leaf morphological characters were analysed through clustering and ordination methods. Putative neutral molecular markers (AFLPs) were used to analyse the molecular variation. Cluster and ordination analyses were also performed on the AFLP markers in addition to calculations of genetic diversity and F-statisitcs. KEY RESULTS: A notable divergence was uncovered between the morphological and molecular analyses. The morphological analysis clearly differentiated individuals into their respective species, whereas the molecular analysis did not. Twenty species-specific AFLP markers were observed from 123 plants in 24 populations but none of these was species-diagnostic. Principal Coordinate Analysis of the AFLP data revealed a clustering, across the first two axes, of individuals according to population rather than according to species. High F(ST) values calculated from AFLP markers also indicated population differentiation (F(ST) = 0.271). Species differentiation accounted for only 13 % of the variation in diversity compared with population differentiation, which accounted for 27 %. CONCLUSIONS: The results show that neutral molecular variation is partitioned more strongly between populations than between species. Although this could indicate that the populations of Q. petraea and Q. robur studied may not be distinct species at a molecular level, it is proposed that the difficulty in distinguishing the species in Irish oak populations using AFLP markers is due to population differentiation masking species differences. This could result from non-random mating in small, fragmented woodland populations. Hybridization and introgression between the species could also have a significant role.     

Origin of spatial genetic structure in an expanding oak population

Spatial genetic structure (SGS) results from the interplay of several demographical processes that are difficult to tease apart. In this study, we explore the specific effects of seed and pollen dispersal and of early postdispersal mortality on the SGS of a seedling cohort (N = 786) recruiting within and around an expanding pedunculate oak (Quercus robur) stand. Using data on dispersal (derived from parentage analysis) and mortality (monitored in the field through two growing seasons), we decompose the overall SGS of the cohort into its components by contrasting the SGS of dispersed (i.e. growing away from their mother tree) vs. nondispersed (i.e. growing beneath their mother tree) and initial vs. surviving seedlings. Patterns differ strongly between nondispersed and dispersed seedlings. Nondispersed seedlings are largely responsible for the positive kinship values observed at short distances in the studied population, whereas dispersed seedlings determine the overall SGS at distances beyond c. 30 m. The paternal alleles of nondispersed seedlings show weak yet significantly positive kinships up to c. 15 m, indicating some limitations in pollen flow that should further promote pedigree structures at short distances. Seedling mortality does not alter SGS, except for a slight increase in the nondispersed group. Field data reveal that mortality in this group is negatively density‐dependent, probably because of small‐scale variation in light conditions. Finally, we observe a remarkable similarity between the SGS of the dispersed seedlings and that of the adults, which probably reflects dispersal processes during the initial expansion of the population. Overall, this study demonstrates that incorporating individual‐level complementary information into analyses can greatly improve the detail and confidence of ecological inferences drawn from SGS.     

Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography

The nuclear genetic variation within and among 21 populations of sessile oak was estimated at 31 RAPD loci in conjunction with previous estimates of variation at eight allozyme loci. The aim of the study was to assess the relative role of isolation-by-distance and postglacial history on patterns of nuclear variation. Because of its small effective population size and maternal transmission, the chloroplast genome is a good marker of population history. Both kinds of nuclear variation (RAPD and allozyme) were therefore compared, first, to the geographical distances among populations and, secondly, to chloroplast DNA restriction polymorphism in the same populations. Multiple Mantel tests were used for this purpose. Although RAPDs revealed less genetic diversity than allozymes, levels of genetic differentiation ( G _ST) were identical. The standard genetic distance calculated at all RAPD loci was correlated with geographical distances but not with the genetic distance calculated from chloroplast DNA data. Conversely, allozyme variation was correlated with chloroplast DNA variation, but not with geography. Possibly, divergent selection at two allozyme loci during the glacial period could explain this pattern. Because of its greater number of loci assayed, RAPDs probably provided a less biased picture of the relative role of geography and history.     

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.     

Using chloroplast DNA to trace postglacial migration routes of oaks into Britain

Postglacial migration is a major factor responsible for the patterns of genetic variation we see in natural populations. Fossil pollen data indicate that early postglacial colonists such as oak, were able to take both western and eastern migration routes into Britain. Analysis at a finer level is now permitted by the use of modern molecular techniques. A 13-bp duplication in the chloroplast tRNA^Leul intron occurs in natural populations of East Anglian oaks, but is not found in other parts of Britain or from mainland Europe. The distribution of this marker suggests that the mutation occurred either in southern England, or during migration from the mainland, and became fixed in a source population from which East Anglia was colonized. Planting of non-native trees for roadside boundaries and in the grounds of old houses and estates, explains the absence of the marker from some East Anglian oaks.     

An evaluation of standard oak tree growth in Ruislip woods, West London

Tree-ring studies on dominant and co-dominant oak standards from four woodlands on the western fringes of London were studied in relation to known historical and meteorological conditions. Whilst previous studies suggested a decline in oak growth in recent decades, this was not apparent from this study. Major recruitment periods for the large oaks were determined. The sites had differing responses to known drought years. Coppicing of the undergrowth was found not to greatly influence the growth of the remaining standard trees on all occasions, although one woodland showed some growth release following recent coppicing. Records of lichens for each woodland were used to assess changing pollution levels at the sites.     

高等植物细胞质雄性不育分子机理的研究进展

从线粒体DNA、叶绿体DNA和线粒体质粒DNA方面较详细地阐述了高等植物细胞质雄性不育的分子机理及最新进展;探讨了细胞核DNA和细胞质DNA之间的相互关系。     

Can invasion patches of Acacia mearnsii serve as colonizing sites for native plant species on Réunion (Mascarene archipelago)?

There is need for documenting the long-term effects of plant invasions at the landscape scale. We investigated the possible catalytic effect of invasive Acacia mearnsii De Wild. on the colonization of rural landscapes by native plant species on Réunion Island (Mascarene Archipelago, Indian Ocean). Data were recorded from 182 circular plots of 50 m² within a set of 48 large invasion patches, aged from 1 to 48+ years. Only eighteen native plant species were present in the invaded patches and these in only 21 of the 48 patches. The Acacia invasion patches colonized by native flora were older and closer to the closest forest remnant. Most invasion patches colonized by native species were located <200 m from forest remnants. Results are consistent with studies on colonization rates of nonindigenous forest plantations, which increase with age and decrease with distance to seeds sources. Yet, the rate of Acacia invasion patches colonized by native flora remained very low compared to studies on the colonization of exotic plantations in other tropical countries. We conclude that invasion patches of Acacia mearnsii are poor colonizing sites for native plant species. Allelopathy is suspected as one of the strongest factors, which prevent this colonization.     

Ten years after: Release cutting around old oaks still affects oak vitality and saproxylic beetles in a Norway spruce stand

1. It is often suggested to release oaks (Quercus robur) from competition, to ensure their survival and boost their conservational value. However, few studies have explored how long-lasting this effect is and how it affects saproxylic beetles.
2. Ten years after cutting, we investigated effects of different release cutting levels (high, medium, and no release) around 140-year-old retained oaks in a commercial forest with Norway spruce (Picea abies).
3. We evaluated oak vitality using crown and dead wood measurements. Saproxylic beetles were caught in window traps, identified to species level, and grouped according to their association with oak and/or Norway spruce.
4. Released oaks had more light, higher temperatures, greater crown growth, and less dead wood in the crown compared to the no-release control.
5. After 10 years we still found a higher abundance of oak-associated beetles and higher overall species richness of saproxylic beetles in the released oaks. Beetle species composition significantly differed between released oaks and control.
6. We suggest avoiding planting trees beneath retained oaks when regenerating conifer forests and to proceed with conservation management during subsequent thinning by removing regeneration under the oak crowns. We emphasize the benefits of monitoring the retained oaks to maintain tree vitality, habitat quality, and insolation.

     

High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

Phylogeography and genetic structure of Hibiscus tiliaceus--speciation of a pantropical plant with sea-drifted seeds

Phylogenetic relationships and the spatial genetic structure of a pantropical plant with sea-drifted seeds, Hibiscus tiliaceus L., and its allied species were investigated. The combined distribution range of these species is over almost the entire littoral area of the tropics worldwide, which might result from the dispersal of their sea-drifted seeds and from recurrent speciation in local populations. A phylogenetic tree constructed using the nucleotide sequences of a c. 7500-bp portion of chloroplast DNA suggested the possibility that recurrent speciation from H. tiliaceus has given rise to all of its allied species. Three major sequence haplotypes of H. tiliaceus had wide and overlapping distributions throughout the Pacific, Atlantic and Indian Ocean regions. This distribution pattern was also confirmed by PCR-SSCP (polymerase chain reaction amplification with single-strand conformation polymorphism) and PCR-SSP (PCR amplification with sequence specific primers) analyses performed on more than 1100 samples from 65 populations worldwide. Statistical analysis using F(ST) and analysis of molecular variance did not show significant genetic differentiation among the H. tiliaceus populations in the three oceanic regions. The results reported here suggested substantial gene flow occurred between populations in the different oceanic regions due to sea-drifted seeds. A strong genetic difference between the Pacific and Atlantic populations of Hibiscus pernambucensis Arruda was observed, which indicates that gene flow in this species between the two regions has been prevented. The wide and dominant distribution of a haplotype shared by H. pernambucensis and H. tiliaceus in the Atlantic region suggests significant introgression between the two species in this region.     

Natural hybridization and introgression of Abies firma and Abies homolepis along the altitudinal gradient and genetic insights into the origin of Abies umbellata

Two Japanese fir species (Pinaceae), Abies firma and A. homolepis, comprise the majority of the temperate forest vegetation zones of Japan. Their vertical distributions are exclusively segregated: A. firma occurs in low elevations and A. homolepis occurs in elevated regions; they contact each other at an altitude of around 1,000–1,100 m. Around the contact zone, A. umbellata is described as a tree with shoots of A. homolepis. It has the greenish cones of A. firma instead of the violet A. homolepis cones. An albinism hypothesis and a hybrid hypothesis were proposed to explain the origin of A. umbellata, provoking long debates. Therefore, we examined a total of 78 A. firma and A. homolepis trees (including an A. umbellata tree) along the altitudinal gradient in two study sites using 13 nuclear microsatellites and a species-specific chloroplast DNA (cpDNA) marker and examined morphologies of shoots and cone scales. Finally, we tested the two hypotheses. The genetic analyses revealed that shoot morphologies of A. homolepis and A. firma correspond mostly to the genetic identity of the species, whereas nine trees with intermediate shoot morphologies and two trees (including the A. umbellata tree) with A. homolepis shoots were genetically intermediate, indicating natural hybrids of A. firma and A. homolepis. These 11 hybrids occur in the narrow altitude ranges of their contact zones. The genetic analyses also suggested that hybrid backcrosses with parental species occur. These results support the hybrid hypothesis and suggest that the natural hybrids should taxonomically be classified as A. × umbellata.     

Selection and dispersal in a multispecies oak hybrid zone

The four western North American red oak species (Quercus wislizeni, Q. parvula, Q. agrifolia, and Q. kelloggii) are known to produce hybrid products in all interspecific combinations. However, it is unknown whether hybrids are transitory resulting from interspecific gene flow or whether they are maintained through extrinsic selection. Here, we examine cryptic hybrid structure in Q. wislizeni through a broad region including contact and isolation from three other western North American red oaks using amplified fragment length polymorphism molecular markers. All four species were simultaneously detected in the genetic background of individuals morphologically assigned to Q. wislizeni, although the contribution of Q. kelloggii was minor. In some cases, introgression was detected well outside the region of sympatry with one of the parental species. Molecular structure at the individual level indicated this was due to long-distance pollen dispersal and not to local extinction of parental species. Species admixture proportions were correlated with climatic variables and greater proportions of Q. agrifolia and Q. parvula were present in the genetic background of Q. wislizeni in sites with cooler and more humid summers, corresponding with habitat preferences of the parental species. Partial Mantel tests indicated that climate was more important than distance from pollen source in this association. Despite high levels of introgression, species integrity was maintained in some populations in close proximity to the other species, providing further support to environmental selection in determining population genetic structure. Thus, the contribution of species mixtures to population genetic structure varies across the landscape according to availability of pollen, but more importantly to varying environmental selection pressures that produce a complex pattern of hybrid and pure gene pools.     

Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical structure, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and temperate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long-term historical continuity has allowed them to maintain a unique store of genetic variation.     

High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland

• Background and Aims Quercus petraea colonized Irelandafter the last glaciation from refugia on mainland Europe. Deforestation,however, beginning in Neolithic times, has resulted in small,scattered forest fragments, now covering less than 12 000 ha. • Methods Plastid (three fragments) and microsatellitevariation (13 loci) were characterized in seven Irish populationssampled along a north–south gradient. Using Bayesian approachesand Wright’s F-statistics, the effects of colonizationand fragmentation on the genetic structure and mating patternsof extant oak populations were investigated. • Key Results All populations possessed cytotypes commonto the Iberian Peninsula. Despite the distance from the refugialcore and the extensive deforestation in Ireland, nuclear geneticvariation was high and comparable to mainland Europe. Low populationdifferentiation was observed within Ireland and populationsshowed no evidence for isolation by distance. As expected ofa marker with an effective population size of one-quarter relativeto the nuclear genome, plastid variation indicated higher differentiation.Individual inbreeding coefficients indicated high levels ofoutcrossing. • Conclusions Consistent with a large effective populationsize in the historical migrant gene pool and/or with high geneflow among populations, high within-population diversity andlow population differentiation was observed within Ireland.It is proposed that native Q. petraea populations in Irelandshare a common phylogeographic history and that the presentgenetic structure does not reflect founder effects.