Comparative leaf surface morphology and molecular data of five oaks of the subgenus Quercus Oerst (Fagaceae)

Abstract

Comparisons between different data sets are important in taxonomic studies, particularly for complex taxa such as the genus Quercus. However, there is scarce literature on comparative morphological and molecular analyses in oaks. Here we describe an experimental approach based on the correlation between micromorphological features and molecular data in order to characterize and discriminate among five closely related species: Q. robur, Q. petraea, Q. frainetto, Q. pubescens and Q. virgiliana.     

Regeneration of oaks (Quercus robur/Q. petraea) and three other tree species during long-term succession after catastrophic disturbance (windthrow)

In broadleaved temperate forests in Europe, oak (Quercus robur/Q. petraea) regeneration is reported to be weak or absent. However, most work concern seedlings or saplings, studied relatively few years. We studied a Picea abies stand in Sweden, windthrown and logged (all stems harvested) in 1969, testing the hypothesis that oaks regenerate in the long term among competing tree species after catastrophic disturbance. In 2011, after 40 years/growth seasons, we recorded live and dead trees in the new stand and investigated the surroundings, competition, and succession. The following trees, up to 26 m tall, colonized: Sorbus aucuparia, Betula pendula/B. pubescens, Fagus sylvatica, Q. robur/Q. petraea, and Corylus avellana (a shrub). Betula dominated, and only Fagus was regenerating in 2011. Sorbus had produced most of the dead trees, mainly or partly through intraspecific competition. In the stand, compared to the surroundings, Quercus, Picea, and Alnus glutinosa were under-represented, and Sorbus, Betula, and Fagus were over-represented. Yet, the density of Quercus was far from negligible; 48 large trees/ha. Most of the oaks (74 %) were co-dominant trees and many grew near Sorbus. Thus, oaks can survive and grow fast among pioneer trees and browsing animals, a conclusion which is supported by the literature (nine studies identified). High mortality of Sorbus is part of a long-term succession, where Fagus might come to dominate. However, Quercus likely will persist, in low density. We propose three key traits contributing to long-term persistence of Q. robur/Q. petraea in European temperate forests: long life span, ecological plasticity, and resistance to disturbances.     

Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

Abstract

In this study, leaf morphology was assessed in a mixed oak stand (western France) using two geometric morphometric (landmark and outline) datasets and one dataset of 19 leaf measures. Adult oaks (817 oaks), comprising four white oak species (Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica), were sampled for DNA extraction and genetic analysis (nuclear microsatellites). Leaf morphology was assessed on 336 oaks, comprising pure species and hybrids as determined by genetic assignment. This comparative study of oak leaf morphology, based on the use of two free size geometric morphometric methods and a set of leaf measurements, combined with the genetic assignment of individuals to pure species or hybrids, provided information about the differences among species and the intermediate leaf morphology of their hybrids.     

Genetic evidence of reproductive isolation in a remote enclave of Quercus pubescens in the presence of cross-fertile species

Peripheral populations may be crucial for understanding processes underlying adaptive genetic variation. Their evolution and ecology are driven by various genetic and demographic processes, such as selection, gene flow and bottleneck. Peripheral populations often experience a reduction in density resulting in the Allee effect. The presence of interfertile species increases the opportunity for hybridisation, which allows for a rescue from the Allee effect, but at the risk of genetic extinction through introgression. In this article we investigated a peripheral population of Quercus pubescens, a European tree species. The study population is located in Poland, several hundred kilometres northwards from the main species range. Due to geographic separation, the study population exists under strong pressure of introgression from potentially inter-fertile Q. petraea and Q. robur, which are the only common oaks in Poland. The intermediate morphology between typical Q. pubescens and a common oak species found in the study population supports the introgression hypothesis, which could be in line with the earlier studies of this species complex conducted in the main range of Q. pubescens. Alternatively, the intermediate morphology could reflect the founder effect or selection at an ecological extreme. We attempted to verify these hypotheses using microsatellites and a reference of common oak species. The results showed that the study population is genetically distinct from both Q. petraea and Q. robur. Additionally, the population is characterised by a low effective population size and limited gene dispersal. This suggests that the study population reveals strong reproductive isolation from common species, implying alternative sources of atypical morphology.     

Role of micromorphological leaf traits and molecular data in taxonomy of three sympatric white oak species and their hybrids (Quercus L.)

Hybridisation and introgression occur with high frequency in the genus Quercus and interspecific hybrid individuals show patterns of morphological traits that might be influenced in different ways. Micromorphological leaf traits appear to be positive and stable in Quercus species, and by combining genetic and micromorphological analyses, it is possible to compare the patterns of variation in micromorphological leaf traits of pure and hybrid individuals. Trichomes and stomatal traits were examined using scanning electron microscopy at 150–2000 × magnification in sympatric oak species collected in a natural deciduous wood. Q. frainetto, Q. petraea and Q. pubescens appear to have a relatively predictable complement of trichome types. Both the pattern and quantitative values of each micromorphological trait examined (stomata and trichomes) have an important role in identifying hybrids and pure species; putative hybrids show a pattern of trichomes that is a combination of the parental types. These results, combined with the fact that micromorphological traits generally exhibit higher consistency, indicate that this source of information can be an excellent clue to hybridisation and introgression and useful in taxonomical, systematic and evolutionary studies on the European white oaks.     

A novel non-symbiotic hemoglobin from oak: Roles in root signalling and development?

The cellular and molecular adaptations of non-model woody species to environmental changes are still poorly understood. We have cloned and characterised a novel non-symbiotic hemoglobin from oak roots (QpHb1) which exhibits a specific cellular distribution in the root. The QpHb1 gene is strongly expressed in the protoderm and the protoxylem cells in two Quercus species (Q. petraea and Q. robur) with contrasting adaptive potential to drought and flooding. The constitutive expression of QpHb1 in both oak species in specific root tissues combined with the reported presence of nitric oxide in the same tissues and its potential for protein S-nitrosylation could support a role for non-symbiotic hemoglobins in signalling changes in the root environment and/or in controlling some aspects of root development.Key words: nonsymbiotic haemoglobin, oak (Quercus), in situ hybridization, signalling, xylem, root, nitric oxide     

Utility of multilocus genotypes for taxon assignment in stands of closely related European white oaks from Switzerland

Background and Aims

European white oaks (Quercus petraea, Q. pubescens, Q. robur) have long puzzled plant biologists owing to disputed species differentiation. Extensive hybridization or shared ancestry have been proposed as alternative hypotheses to explain why genetic differentiation between these oak species is low. Species delimitation is usually weak and often shows gradual transitions in leaf morphology. Hence, individual identification may be difficult, but remains a critical step for both scientific work and practical management.

Methods

Multilocus genotype data (five nuclear microsatellites) were used from ten Swiss oak stands for taxon identification without a priori grouping of individuals or populations, using model-based Bayesian assignment tests.

Key Results

Three groups best structured the data, indicating that the taxonomical signal was stronger than the spatial signal. Most individuals showed high posterior probabilities for either of three genetic groups that were best circumscribed as taxonomical units. The assignment of a subset of trees, whose taxonomic status had been previously characterized in detail, supported this classification scheme.

Conclusions

Molecular-genetic assignment tests are useful in the identification of species status in critical taxon complexes such as the European white oaks. Such an approach is of practical importance for forest management, e.g. for stand certification or in seed trade to trace the origin of forest products.Key words: Assignment test, Bayesian inference, multilocus genotype, nuclear microsatellites, Quercus sp., species complex     

Patterns of contemporary hybridization inferred from paternity analysis in a four-oak-species forest

Background  

Few studies address the issue of hybridization in a more than two-species context. The species-rich Quercus complex is one of the systems which can offer such an opportunity. To investigate the contemporary pattern of hybridization we sampled and genotyped 320 offspring from a natural mixed forest comprising four species of the European white oak complex: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto.     

Changes in the Dynamics of Foliar N Metabolites in Oak Saplings by Drought and Air Warming Depend on Species and Soil Type

Climate change poses direct or indirect influences on physiological mechanisms in plants. In particular, long living plants like trees have to cope with the predicted climate changes (i.e. drought and air warming) during their life span. The present study aimed to quantify the consequences of simulated climate change for foliar N metabolites over a drought-rewetting-drought course. Saplings of three Central European oak species (i.e. Quercus robur, Q. petraea, Q. pubescens) were tested on two different soil types (i.e. acidic and calcareous). Consecutive drought periods increased foliar amino acid-N and soluble protein-N concentrations at the expense of structural N in all three oak species. In addition, transient effects on foliar metabolite dynamics were observed over the drought-rewetting-drought course. The lowest levels of foliar soluble protein-N, amino acid-N and potassium cation with a minor response to drought and air warming were found in the oak species originating from the driest/warmest habitat (Q. pubescens) compared to Q. robur and Q. petraea. Higher foliar osmolyte-N and potassium under drought and air warming were observed in all oak species when grown on calcareous versus acidic soil. These results indicate that species-specific differences in physiological mechanisms to compensate drought and elevated temperature are modified by soil acidity.     

First dendrochronological studies of Quercus protoroburoides

Quercus protoroburoides Donchev and Bouzov ex Tashev and Tsavkov (Rila oak) is a species with extremely limited and localized distribution. It is found only on several locations on slopes above Rila Monastery in Rila Mountains (Bulgaria) at elevations between 1500 m and 1750 m a.s.l. The trees are in small groups or scattered, usually situated on ridges slightly higher than the local population of sessile oak (Quercus petraea (Matt.) Liebl.) and above mixed fir-beech forests. The species was first discovered and described in 1968 by Boris Buzov, but was officially validated in 2017 by Tashev and Tsavkov. Up to this moment there were no dendrochronological studies of the species and there is general lack of data on how climate affects its growth. Our aim was to contribute to filling this knowledge gap. In our study we analyzed 42 series (22 trees) from Q. protoroburoides from two locations (Drushlyavitsa and Brichebor) and compared them to cores from Q. petraea from the same region. The Rila oak trees varied in age from 30 to 170 years. Nearly half of them were about 50 years old. The composed tree-ring chronology spans from 1856 to 2019 with more than 5 included series after 1870. The sessile oak trees were generally older and the chronology spanned from 1743, having more than 4 series after 1786. The climate-growth analysis with local and gridded data revealed positive effects on growth of previous August and current April-June precipitation, positive correlations with previous May-June temperatures and negative with August temperatures. Most of the pointer years with low growth were characterized by extreme climate conditions, such as summer droughts, unusually cold summers or delayed start of the vegetation period due to late frost events at the end of May or early June. Our data indicate that Q. protoroburoides and Q. petraea trees at this unusually high location for oaks are sensitive to climate conditions including summer droughts.     

Differential ecophysiological responses to seasonal drought of three co-existing oak species in northern Greece

Oaks (Quercus spp.) represent the most important broadleaf genus with respect to forest-shaping tree species in the Mediterranean. Considering future climate scenarios (increased drought conditions), the identification of drought tolerant oak species is of great importance for future forest management in this region. The objective of the study was the comparison of physiological status of three economically and ecologically valuable oak species (Quercus ilex, Quercus frainetto and Quercus pubescens) co-existing in natural coppice stands in NE Greece, in response to seasonal drought stress. Measurements were conducted between June and September 2016, every 15–20 days until leaf falling. The parameters studied were predawn leaf water potential and fast chlorophyll fluorescence induction curves (OJIP test), chlorophyll content, and relative water content. Meteorological data from the area were also collected. Photosynthetic parameters such as performance indices (PI_abs and PI_tot) reacted to summer drought conditions, with Q. frainetto showing the lowest values. The discrepancy between species increased with duration of drought period. Q. frainetto revealed the lowest predawn water potential values. The results indicate that Q. frainetto is less suitable for future forestry applications in the studied climate/elevation zone than Q. pubescens and Q. ilex.     

Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species

Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same features, however, make oak communities suited for the study of speciation, hybridization, and genetic adaptation. Efforts to develop new and to adapt existing genomic resources to less-studied members of this genus should not only improve oak conservation and management but also aid the study of fundamental evolutionary processes. Here, we present a suite of 27 highly polymorphic simple sequence repeat (SSR) markers tested in four North American red oak (Quercus section Lobatae) species: Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina. Five markers are genomic SSRs (gSSRs) — four novel and one previously transferred from Q. petraea — and 22 are gene-based SSRs derived from Q. robur and Q. petraea expressed sequence tags (EST-SSRs). Overall, levels of polymorphism detected with these primer pairs were high, with gene diversity (H _e) averaging 0.66 across all loci in natural populations. In addition, we show that EST-SSR markers may have the potential to detect divergent selection at stress-resistance candidate genes among closely related oak species.     

Single‐nucleotide polymorphism discovery and validation in high‐density SNP array for genetic analysis in European white oaks

An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full‐sib progenies (one within each species and two interspecific crosses between Q. petraea and Q. robur) and three natural populations from south‐western France that included two additional interfertile white oak species (Q. pubescens and Q. pyrenaica). The genotyping success rate in mapping populations was 80.4% overall and 72.4% for polymorphic SNPs. In natural populations, these figures were lower (54.8% and 51.9%, respectively). Illumina genotype clusters with compression (shift of clusters on the normalized x‐axis) were detected in ~25% of the successfully genotyped SNPs and may be due to the presence of paralogues. Compressed clusters were significantly more frequent for SNPs showing a priori incorrect Illumina genotypes, suggesting that they should be considered with caution or discarded. Altogether, these results show a high experimental error rate for the Infinium array (between 15% and 20% of SNPs potentially unreliable and 10% when excluding all compressed clusters), and recommendations are proposed when applying this type of high‐throughput technique. Finally, results on diversity levels and shared polymorphisms across targeted white oaks and more distant species of the Quercus genus are discussed, and perspectives for future comparative studies are proposed.     

Taxonomic identity of Quercus coccifera L. in the Iberian Peninsula is maintained in spite of widespread hybridisation, as revealed by morphological, ISSR and ITS sequence data

Interspecific introgression is a well-known phenomenon in oaks whose ecological and evolutionary consequences, although relevant, are still unclear. We investigated molecular variation and any evidence for hybridisation in nine natural populations of kermes oak (Quercus coccifera L.) from the Iberian Peninsula. Additive patterns in 59 nrDNA ITS sequences revealed that hybrid individuals showing intermediate genotypes between kermes and holm (Q. ilex L.) oaks are very frequent, although intermediate morphotypes are uncommon. Bayesian analysis of ISSR fingerprinting patterns indicated extensive gene-flow among Q. coccifera populations and neighbouring Quercus taxa. Introgression appeared to be an active mechanism in the pair Q. coccifera–Q. ilex, but no conclusive evidence supporting hybridisation between Q. coccifera and other co-occurring Quercus species was found. The role of canalisation in the maintenance of stable morphological characters in the face of extensive introgression is discussed.     

Extent of nuclear genome sharing among white oak species (Quercus L. subgen. Lepidobalanus (Endl.) Oerst.) in Slovakia estimated by allozymes

European white oak species (Quercus subg. Lepidobalanus) are known to share a substantial part of the nuclear and cytoplasmic genome. In spite of this fact, they have preserved their integrity. We analyzed genetic variation at thirteen isozyme loci in nine Quercus robur, ten Q. petraea, two Q. pubescens and two mixed (two-species) populations in Slovakia to assess the extent of allele sharing. Moreover, a detailed morphometric study based on thirteen leaf traits was done in the mixed stands. A Bayesian analysis of population structure in the set of pure populations revealed the existence of three clusters, which coincided with the supposed taxonomical identity of populations. However, the distribution of posterior probabilities of data was bimodal with a second peak at six groups, what indicates a possible substructure in the gene pools of the investigated oak species. Moreover, gene admixture was close to 50% in all investigated populations. Morphometric analysis of the two mixed stands revealed a clear morphological separation of the studied oak species, sharply contrasting with a high degree of gene admixture. Differentiation is not uniformly distributed over the genome. High levels of differentiation (F _ST > 0.10) were observed at only three out of thirteen loci. The hypotheses explaining extensive allele sharing (shared ancestral polymorphisms vs. high levels of interspecific gene flow) are briefly discussed.     

Different ability of three Mediterranean oak species to tolerate progressive water stress

Inter-comparisons in the gas exchange patterns and root characteristics under both well-watered and drought conditions were done in three-years-old seedlings of three oak species (Quercus cerris L., Q. frainetto Ten., and Q. ilex L.) growing in controlled environment. Well-watered Q. cerris had greater physiological performances than other oaks, but under drought it was not able to face the water stress showing also structural modifications such as reduction of root length and average diameter. On the other hand, Q. ilex maintained root growth both in drought or well-watered soils. Moreover, it was able to keep open stomata also under water stress, although stomatal conductance (g _s) was low. Q. frainetto had an intermediate position in regard to its physiological and root structural characteristics between Q. cerris and Q. ilex under drought stress. For all oaks the relationship between g _s and the ratio of sub-stomatal and ambient CO₂ concentration (C _i/C _a) highlighted the dynamic adaptation of g _s to the increase of hydraulic resistances of leaf, stem, and roots portions, more evident during the air humidity change and progressive soil dehydration. This suggests a well-triggered above-and under-ground mechanism to endure the drought stress.     

Linkage mapping of osmotic stress induced genes of oak

Water stress affecting long-lived trees is an important challenge in forestry. Due to global climate change, forest trees will be threatened by extreme conditions like flooding or drought. It is necessary to understand differences in stress tolerance within certain species and to investigate putative relations on genomic level. In this study, osmotic stress induced genes of Quercus ssp. were positioned on two genetic linkage maps of oak. An intra-specific cross 3P*A4 of Quercus robur consisting of 88 offspring and an inter-specific cross 11P*QS29 of Q. robur and Q. petraea comprising 72 full-sibs were analyzed for the inheritance of 14 loci represented by 34 individual single nucleotide polymorphisms. Seven genes in the intra-cross, as well as other six genes in the inter-cross could be mapped and one gene could not be localised due to the severe distortion of the segregation. The collection of expressed sequences involved ribosomal proteins, members of the oxylase/oxygenase gene family, betaine aldehyde dehydrogenase, Dc3 promoter-binding factor, a putative member of the nodulin family, glutathione-S-transferase and proteins with unknown functions. In the inter-cross, two linked markers exhibited 89% deficiency of heterozygosity. Thirteen genes were positioned on ten different oak chromosomes and can serve as orthologous markers in comparative mapping studies within Fagaceae.     

Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes

Bayesian clustering methods have been widely used for studying species delimitation and genetic introgression. In order to test the effect of phylogenetic relationships and sampling scheme on the inferred clustering solution and on the performance of Bayesian clustering analysis, I simulated genotypes of the interfertile oak species Quercus robur, Quercus petraea, and Quercus pubescens and I run analyses using two popular software programs, STRUCTURE and BAPS. First, based on purebred simulations, I compared clustering solutions resulting from different sample size configurations. While clustering solution generally reflected the taxonomic relationships when equal samples of each species were included, spurious partition was inferred by STRUCTURE when some species were represented by larger and others by smaller samples. In very unbalanced configurations, STRUCTURE failed to identify the three species, even if three subpopulations were assumed. By contrast, BAPS could properly identify the three species under any sampling scheme. Second, based on simulations of purebreds and hybrids, I tested the performance of individual assignments with variable number of loci. This analysis showed that STRUCTURE can detect introgressed individuals more efficiently than BAPS. However, BAPS could assign purebreds more efficiently with a lower number of loci. Method performance also depended on phylogenetic relationships. In the case of Q. petraea, Q. pubescens, and their hybrids, method performance was lower due to their phylogenetic affinity. Inclusion of three instead of two species into the analysis led to reduction of performance, and to misclassification of hybrids, which often reflected the phylogenetic affinity between Q. petraea and Q. pubescens.     

Insights into drought adaptation of two European oak species revealed by nucleotide diversity of candidate genes

Nucleotide diversity, correlations to environmental conditions, and deviations from standard neutral models were examined in eight candidate genes for drought response of European oaks Quercus petraea and Quercus robur. Baseline genetic parameters were calculated and deviation from neutrality was tested using Tajima’s D, and Fu and Li’s D and F statistics. Population structure was investigated using differentiation indices and Bayesian clustering. Similar values of total nucleotide diversity were found in both species with significant higher diversity at non-synonymous sites in Q. robur while the number of haplotypes was significantly higher in Q. petraea. Significant population differentiation was found for three genes in Q. petraea and for one gene in Q. robur. Within four genes, strong correlations were found between the local temperature–precipitation regime and the allele frequencies of six alleles, of which three were private to Q. petraea. Using various population genetic and Bayesian tests for neutrality, four outlier single nucleotide polymorphisms (SNPs) under putative selection were detected in two of the analyzed genes. Significant differentiation and strong allelic correlation to environmental conditions support preceding gene expression profiling experiments, where functional impact of candidate genes in drought response has been revealed. Q. petraea populations were found to be more differentiated as compared to Q. robur—this could be linked to the higher adaptive potential of this species under arid conditions.