Phylogenetic relationships in Chinese oaks (Fagaceae,Quercus): Evidence from plastid genome using low-coverage whole genome sequencing

China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.     

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.     

Evidence for hybridization and introgression within a species-rich oak (<Emphasis Type="Italic">Quercus</Emphasis> spp.) community

Background  

Analysis of interspecific gene flow is crucial for the understanding of speciation processes and maintenance of species integrity. Oaks (genus Quercus, Fagaceae) are among the model species for the study of hybridization. Natural co-occurrence of four closely related oak species is a very rare case in the temperate forests of Europe. We used both morphological characters and genetic markers to characterize hybridization in a natural community situated in west-central Romania and which consists of Quercus robur, Q. petraea, Q. pubescen s, and Q. frainetto, respectively.     

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.     

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.     

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.     

Hybridization and divergence in multi‐species oak (Quercus) communities

Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post‐zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q. ellipsoidalis and Q. velutina. Overall, c. 20% of Q. velutina had recent ancestry from Q. ellipsoidalis, whereas nearly 30% of Q. ellipsoidalis had a Q. velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene‐linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15‐cM bin on an existing Q. robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression.     

桂西地区南亚热带落叶栎林群落组成及物种多样性研究北大核心CSCD

落叶栎林是桂西地区南亚热带的典型次生林,也是该区域落叶阔叶林的重要群系组。该研究采用典型样方法对桂西地区落叶栎林群落进行调查,分析了该区域落叶栎林群落的物种组成、区系成分、物种多样性特征及其与地形因子的关系,为桂西地区南亚热带植物多样性保护与恢复提供依据。结果显示:(1)研究区落叶栎林群落维管束植物共计269种,隶属80科178属。(2)种子植物区系以热带成分为主,同时表现出一定程度的温带过渡性质。(3)聚类分析表明,调查的落叶栎林群落可分为云南波罗栎林、栓皮栎林、白栎林、麻栎林4种林分类型,其中以白栎林群落的物种多样性最高,且灌木层的物种多样性显著高于乔木层和草本层。(4)RDA分析显示,落叶栎林群落不同层次物种多样性的差异受地形因子的影响,多样性指标与经度、纬度、海拔之间具有明显的相关性(P<0.05),其中乔木层物种多样性主要与经度、纬度呈显著的相关性,灌木层物种多样性与纬度、海拔相关,草本层物种多样性与经度、纬度、海拔之间均有相关性。     

Osmotic stress responses of individual white oak (Quercus section, Quercus subgenus) genotypes cultured in vitro

White oaks (Quercus section, Quercus subgenus) are widely distributed in Europe. Quercus petraea (sessile oak), an economically important species is predicted to be affected by climate change. Q. pubescens (pubescent oak) and Q. virgiliana (Italian pubescent oak) are economically less important, drought tolerant species. Frequent hybridization of white oaks was observed and currently the introgression of Q. pubescens and Q. virgiliana in non-mediterranean regions of Europe has been reported. Our goal was to use tissue cultures established from individual trees of the above taxa and their putative hybrids, all present in the forest stand of Síkf?kút LTER Research Area (NE Hungary) as simple experimental model systems for studying drought/osmotic stress tolerance. Tissue cultures are more suitable models for such studies, than seedlings, because they are genetically identical to the parent plants. Polyethylene glycol (PEG6000) treatments were used for this purpose. The identification of taxa was based on leaf morphological traits and microsatellite analysis and showed that Q. petraea is genetically distinct to all other taxa examined. We established six callus lines of Quercus. As expected, in Q. petraea cultures PEG6000 induced severe loss of fresh weight and the ability to recover after removal of the osmoticum, which was not characteristic for Q. pubescens and Q. virgiliana. Putative hybrids exhibited an intermediate response to osmotic stress. Activity gels showed the increase of single-strand preferring (SSP) nuclease and no significant change of guaiacol-peroxidase activities in drought-sensitive genotypes/cultures and no significant increase of SSP nuclease activities accompanied with increases of guaiacol-peroxidase activities in drought-tolerant ones. This indicates that drought/osmotic stress tolerance is associated to increased capacity of scavenging reactive oxygen species and hence less susceptibility to DNA damage. Our results confirm that tissue cultures of oak are suitable model systems for studying drought/osmotic stress responses.     

Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long‐standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar‐cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first‐ and later‐generation hybrids, identifying 124 interspecific hybrids from a collection of 2,991 coral trout sampled in inshore and mid‐shelf reefs of the southern Great Barrier Reef. Hybrids were ubiquitous among reefs, fertile and spanned multiple generations suggesting both ecological and evolutionary processes are acting to maintain species barriers. We elaborate on these finding to investigate the extent of genomic introgression and admixture from 2,271 SNP loci recovered from a ddRAD library of pure and hybrid individuals. An analysis of genomic clines on recovered loci indicates that 261 SNP loci deviate from a model of neutral introgression, of which 132 indicate a pattern of introgression consistent with selection favouring both hybrid and parental genotypes. Our findings indicate genome‐wide, bidirectional introgression between two sympatric species of coral reef fishes and provide further support to a growing body of evidence for the role of hybridization in the evolution of coral reef fishes.     

Prey distribution,foliage structure,and foraging behavior of insectivorous birds in two oak species (<Emphasis Type="Italic">Quercus serrata</Emphasis> and <Emphasis Type="Italic">Q. variabilis</Emphasis>)

We examined foraging behaviors of four insectivorous bird species (Great Tit Parus major, Varied Tit P. varius, Long-tailed Tit Aegithalos caudatus and Japanese White-eye Zosterops japonica) on the two oak species (Q. serrata and Q. variabilis) in relation to fine-scale foliage structures, abundance, and distribution of folivorous insects and physical and chemical characteristics of leaves. There was no difference in the mean number of insects for each oak species, but there was a significant difference in the mean biomass. The distance from twigs or branches to leaf tips or blade-petiole junctions showed that leaves of Q. variabilis were more dispersed than those of Q. serrata. The different size distribution of insects influenced insect sizes selected and foraging maneuvers used by each bird species. Parus major and P. varius fed on beetles (low energy gain) with perch-gleaning (the most energy-saving maneuver) from the upper side of leaves on Q. variabilis, whereas they fed on large lepidopteran larvae (high energy gain) from the lower side of leaves on Q. serrata using a variety of maneuvers (including energy-consuming ones). Both A. caudatus and Z. japonica fed on insects from the lower side of leaves by hang-gleaning and reach-gleaning, respectively. These species appeared to be morphologically adapted to the energy-consuming but more effective maneuvers used to take preys from the undersides of leaves. We hypothesize that differences in foliage structures between closely related species of trees have evolved as a balance between defense against folivorous insects and attraction of insectivorous birds.     

Limited hybridization between Quercus lobata and Quercus douglasii (Fagaceae) in a mixed stand in central coastal California

Many oak species are interfertile, and morphological and genetic evidence for hybridization is widespread. Here we use DNA microsatellite markers to characterize hybridization between two closely related oak species in a mixed stand in central coastal California, Quercus lobata (valley oak) and Q. douglasii (blue oak) (Fagaceae). Genotypes from four microsatellite loci indicate that many alleles are shared between the two species. However, each species harbors unique alleles, and allele frequencies differ significantly. A Bayesian analysis of genetic structure in the stand identified two highly differentiated genetic clusters, essentially corresponding to species assignment based on morphology. Data from the four loci were sufficient to assign all 135 trees to one of the two species. In addition, five putative hybrid individuals having intermediate morphologies could be assigned genetically to one or the other species, and all but one had low probability of hybrid ancestry. Overally, only six (4.6%) trees showed >0.05 probability of hybrid ancestry, in all cases their probabilities for nonhybrid ancestry were substantially higher. We conclude that adult hybrids of Q. douglasii × Q. lobata are rare at this site and plasticity in morphological characters may lead to overestimates of hybridization among Quercus species.     

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.     

Not only size matters: Acorn selection by the European jay (Garrulus glandarius)

A strong selection for acorn characteristics is expected to have evolved in the mutualistic relationship between the European jay (Garrulus glandarius) and the oak (Quercus spp.). Bossema's pioneer work suggested that jays do not select acorns randomly, but rather they preferentially select some size and species. Preference for some seeds over others may have implications on plant community dynamics by conferring advantages (or disadvantages) on the selected (avoided) seed characteristics. In this paper we test to what extent jays select acorns by species and/or by size and the relation between these two traits in Mediterranean oak species. The experiments consist of a set of field tests in which acorns from four different coexisting Mediterranean oak species (Quercus ilex, Quercus faginea, Quercus suber, and Quercus coccifera) were placed in artificial feeders accessible to wild jays. The acorns were previously measured to control individual acorn characteristics. Using video-recording techniques, we followed jay activity and the fate of each acorn (sequence of acorn selection and method of transport). Q. ilex acorns were preferred over other acorns, and Q. coccifera acorns were avoided when other acorns were available. Preference for Q. faginea and Q. suber acorns was intermediate, that is, they were preferred over Q. coccifera acorns but not over Q. ilex acorns. Large acorns were also preferred although acorn species selection was stronger than size selection. Jays selected species and size both by visual means and by using acorn area as an indicator of size. Acorns wider than 17–19 mm were carried in the bill because of throat limitation. Our results confirm Bossema's study on temperate oaks and extend it to Mediterranean oak species, revealing implications on mixed oak forest dynamics.     

Factors affecting stress tolerance in recalcitrant embryonic axes from seeds of four Quercus (Fagaceae) species native to the USA or China

MethodsWater relations and survival of excised axes in response to water loss and cryo-exposure were compared for four Quercus species from subtropical China (Q. franchetii, Q. schottkyana) and temperate USA (Q. gambelii, Q. rubra).ConclusionsQuercus species adapted to arid and semi-humid climates still produce recalcitrant seeds. The ability to avoid freezing rather than drought may be a more important selection factor to increase desiccation tolerance. Cryopreservation of recalcitrant germplasm from temperate species is currently feasible, whilst additional protective treatments are needed for ex situ conservation of Quercus from tropical and subtropical areas.     

Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico

Background and Aims

Interspecific gene flow can occur in many combinations among species within the genus Quercus, but simultaneous hybridization among more than two species has been rarely analysed. The present study addresses the genetic structure and morphological variation in a triple hybrid zone formed by Q. hypoleucoides, Q. scytophylla and Q. sideroxyla in north-western Mexico.

Methods

A total of 247 trees from ten reference and 13 presumed intermediate populations were characterized using leaf shape variation and geometric morphometrics, and seven nuclear microsatellites as genetic markers. Discriminant function analysis was performed for leaf shape variation, and estimates of genetic diversity and structure, and individual Bayesian genetic assignments were obtained.

Key Results

Reference populations formed three completely distinct groups according to discriminant function analysis based on the morphological data, and showed low, but significant, genetic differentiation. Populations from the zone of contact contained individuals morphologically intermediate between pairs of species in different combinations, or even among the three species. The Bayesian admixture analysis found that three main genetic clusters best fitted the data, with good correspondence of reference populations of each species to one of the genetic clusters, but various degrees of admixture evidenced in populations from the contact area.

Conclusions

The three oak species have formed a complex hybrid zone that is geographically structured as a mosaic, and comprising a wide range of genotypes, including hybrids between different species pairs, backcrosses and probable triple hybrids.     

Interspecific hybridization between greater kudu and nyala

Hybridization of wildlife species, even in the absence of introgression, is of concern due to wasted reproductive effort and a reduction in productivity. In this study we detail an accidental mating between a female nyala (Tragelaphus angasii) and a male greater kudu (T. strepsiceros). The hybrid was phenotypically nyala and was identified as such based on mitochondrial DNA. Further genetic analysis based on nine microsatellite markers, chromosome number and chromosome morphology however, confirmed its status as an F1 hybrid. Results obtained from a reproductive potential assessment indicated that this animal does not have the potential to breed successfully and can be considered as sterile.     

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.     

Structure of herbivore communities in two oak (Quercus spp.) hybrid zones

Summary We examined patterns of density and species diversity for leaf-mining Lepidopterans and gall-forming Hymenopterans in two oak (Quercus spp.) hybrid zones: Quercus depressipes x Q. rugosa and Q. emoryi x Q. coccolobifolia. In both species complexes, hybrid hosts typically supported significantly lower densities and species diversity of parasites than did parental types. This contradicts the findings of Whitham (1989) that suggested that hybrid hosts may act as parasite sinks both in ecological and evolutionary time. We discuss features of hybrid zones that are likely to influence patterns of herbivory.