Find research datasets worth reusing

opencc-zeroJul 2020View details →

Data from: Contrasting species decline but high sensitivity to increasing water stress on a mixed pine-oak ecotone

1. Forest decline under environmental stress is expressed by regeneration failure and accelerated mortality in all ontogenic stages at the population level. Characterizing functional traits and mechanisms that best capture species decline and mortality is essential to assess forest dynamics. 2. We analyzed sensitivity to increasing water stress in two species with different water-use strategies on a mixed Quercus pyrenaica - Pinus sylvestris forest where adult pines express vulnerability to climate change but oaks do not. We compared dynamics of radial growth, wood δ13C and sapwood nonstructural carbohydrates (NSC) in response to drought at different time scales in both species and two age-cohorts in pine. 3. Both species were very sensitive to water stress, which influenced trait phenotypic plasticity at short- and long-time scales. Water-use strategy in pines of both ages was more conservative than in the more drought-tolerant oak. Both species showed negative growth trends despite increasing iWUE. Recent growth of pines is slower than it was in the past. Carbon isotope discrimination trends in young pines suggested increasing leaf gas exchange constraints. NSC were far from depletion in both species and all pine ages. Intra- and inter-annual NSC variability was higher in oaks than in pines and in soluble sugars (SS) than in starch. SS were lowest in young pines. Sensitivity of NSC to contrasting climatic years was low in pines, which NSC mostly remained homeostatic. The sensitivity to climate expressed suggests different C-allocation strategies, with less coupling between radial growth and current year photosynthesis in young pines. 4. Synthesis. Pines expressed negative responses to increased water stress regardless of age, showing rising gas-exchange constraints through tighter stomatal control of water losses than oaks. Young pines showed similar functional responses to water stress than old pines in decline, which suggests species-level vulnerability and could be regarded as early-warning signals anticipating mortality in pines. Yet, given the high sensitivity to drought also expressed by the non-declining oak, it would have been difficult to unequivocally disentangle species decline based only on the traits analysed.

opencc-zeroDec 2016View details →

Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.

opencc-zeroDec 2018View details →

Data from: Influence of a climatic gradient on genetic exchange between two oak species

Premise of the study. In plant groups with limited intrinsic barriers to gene flow, it is thought that environmental conditions can modulate interspecific genetic exchange. Oaks are known for limited barriers to gene flow among closely related species. Here, we use Quercus as a living laboratory in which to pursue a fundamental question in plant evolution: do environmental gradients restrict or promote genetic exchange between species? Methods. We focused on two North American oaks, the rare Q. dumosa and the widespread Q. berberidifolia. We sampled intensively along a contact zone in California. We sequenced restriction site associated DNA markers and measured vegetative phenotype. We tested for genetic exchange, the association with climate, and the effect on phenotype. Key results. There is evidence for genetic exchange between the species. Admixed plants are found in areas of intermediate climate, while less admixed plants are found at the extremes of the climatic gradient. Genetic and phenotypic patterns are out of phase in the zone of contact; some plants display the phenotype of one species but are genetically associated with another. Conclusions. Our results support the hypothesis that a strong climatic gradient can promote genetic exchange between species. The overall weak correlation between genotype and phenotype in the contact zone between the species suggests that genetic exchange can lead to the breakdown of trait combinations used to define species. This incongruency predicts ongoing problems for conservation of Q. dumosa, with implications for conservation of other oaks. Please be aware that if you ask to have your user record removed, we will retain your name in the records concerning manuscripts for which you were an author, reviewer, or editor. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r) Please contact the publication office if you have any questions.

Fig. 12 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America

Fig. 12. Distribution of species of the genera Crassomiris, Phallospinophylus, and Pygovepres.

Fig. 13 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America

Fig. 13. Distribution of species of the genera Quercophylus, Rubellomiris, and Rubeospineus.

Fig. 3 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America

Fig. 3. Head and male genitalic structures of Crassomiris spp. and Phallospinophylus setosus.

Fig. 2 in New Genera and Species of Oak-Associated Phylini (Heteroptera: Miridae: Phylinae) from Western North America

Fig. 2. Habitus photographs of Rubellomiris spp. and Rubeospineus spp.

opencc-by-4.0Jan 2024View details →

The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China

Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.

opencc-zeroDec 2021View details →

Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta

Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra- and interspecific differentiation patterns is of great significance to understanding speciation. The genus Quercus is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in the white oak Quercus laeta, some corresponding to the previously described species Q. centralis, Q. laeta, Q. prinopsis and Q. transmontana, as well as geographically structured variation within Q. transmontana not previously described. Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation. Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed. Morphological differences were evaluated using geometric morphometrics. Chloroplast DNA showed low differentiation, suggesting introgression or sharing of ancestral haplotypes among the Q. laeta morphotypes. Nuclear microsatellites indicated differentiation into two distinct main genetic groups, which were congruent with morphological differentiation. In conclusion, nuclear markers and morphological variation suggest the existence of at least two different entities within Q. laeta.

opencc-zeroFeb 2022View details →

Aboveground herbivory causes belowground changes in twelve oak Quercus species: a phylogenetic analysis of root biomass and non‐structural carbohydrate storage

Plant ecosystem structure is understood to be a result of complex multitrophic interactions. Most multitrophic studies focus on plant aboveground adaptations to aboveground herbivore pressures, neglecting belowground adaptations in response to aboveground damage. Differential investment in root structures may allow plants to compensate for tissue loss or damage due to herbivores. Furthermore, phylogeny may constrain a plant's ability to adapt belowground. We examined the belowground responses of 12 species of oak (Quercus) to varying locations and intensities of simulated herbivore damage. We first established that oak belowground traits responded to aboveground herbivory by measuring patterns of investment in coarse vs fine root structures and re-allocation of non-structural carbohydrates (NSC) to root storage. We then tested whether phylogeny could explain variations in investment patterns using phylogenetic independent contrasts. Plant adaptations to aboveground herbivory included allocating biomass and carbon reserves to root structures, depending on the location and intensity of herbivore damage. NSC re-allocation to root storage was observed when oak species experienced any type of damage, but damage to lateral tissues caused a greater re-allocation than apical damage or control treatments. We found that most belowground responses to aboveground herbivory are species-specific and may be adapted for environmental conditions or type of herbivory. Some responses to herbivore damage, such as changes in fine-root mass and root sugar concentrations, were phylogenetically constrained. Phylogenetic constraints generally occur when there is severe damage at the apical meristem. Plants may adapt to aboveground tissue loss due to varying herbivore pressures (i.e. varying location and intensity of damage) by differentially investing in root types and NSC re-allocation to root storage. Understanding linkages between and phylogenetic constraints of plant belowground responses to aboveground herbivory will improve our understanding of the ecological processes involved in multitrophic interactions.

opencc-zeroSep 2022View details →

Growth, defense, and storage responses of 12 oak (Quercus) species to varying locations and intensities of simulated herbivory

The evolution of plant defenses is often constrained by phylogeny. Many of the differences between competing plant-defense theories hinge upon the differences in the location of meristem damage (apical vs. auxiliary) and the amount of tissue removed. We analyzed the growth and defense responses of 12 Quercus (oak) species from a well-resolved molecular phylogeny using phylogenetically independent contrasts. Access to light is paramount for forest-dwelling tree species, such as many members of the genus Quercus. We therefore predicted a greater investment in defense when apical meristem tissue was removed. We also predicted a greater investment in defense when large amounts of tissue were removed and a greater investment in growth when less tissues were removed. We conducted five simulated-herbivory treatments including a control with no damage and alterations of the location of meristem damage (apical vs. auxiliary shoots) and intensity (25% vs. 75% tissue removal). We measured growth, defense, and nutrient re-allocation traits in response to simulated herbivory. Phylomorphospace models were used to demonstrate the phylogenetic nature of trade-offs between characteristics of growth, chemical defenses, and nutrient re-allocation. We found that growth-defense trade-offs in control treatments were under phylogenetic constraints, but phylogenetic constraints and growth-defense trade-offs were not common in the simulated-herbivory treatments. Growth-defense constraints exist within the Quercus genus, although there are adaptations to herbivory that vary among species.

opencc-by-4.0Jul 2024View details →

The alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species

This dataset includes the alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species. The alignment was generated through four steps: (1) We used PhyloSuite v.1.2.2 to extract protein-coding genes (PCGs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) from the plastomes of 761 East Asian Cerris oak trees and 29 accessions of 22 related oak species. (2) The extracted regions were aligned individually with MAFFT v.7.313 and adjusted manually using BioEdit v.7.2.5. Specifically, inversions and length variations in simple sequence repeats were excluded because of their tendency for homoplasy. Eight ambiguously aligned regions in rps16-trnQ, psbM-trnD, ndhF-rpl32, rpl32-trnL, ndhD-psaC, and psaC-ndhE IGSs, and ndhF and ycf1 PCGs were also discarded to reduce phylogenetic noise. (3) The individual alignments were concatenated according to their respective positions in the plastome to generate a whole-plastome alignment with only one inverted repeat (IR) retained. (4) Unique plastome haplotypes were determined by DnaSP v.5.10.01.

opencc-by-4.0Nov 2006View details →

Figures 4–6 in The Western Palaearctic species of Psilophrys Mayr (Hymenoptera, Chalcidoidea: Encyrtidae), parasitoids of kermesids (Hemiptera, Coccoidea: Kermesidae) attacking oaks (Quercus spp.)

Figures 4–6. Psilophrys bella, ♀. (4) Ovipositor. (5) Antenna. (6) Fore wing.

opencc-by-4.0Nov 2006View details →

Figures 1–3 in The Western Palaearctic species of Psilophrys Mayr (Hymenoptera, Chalcidoidea: Encyrtidae), parasitoids of kermesids (Hemiptera, Coccoidea: Kermesidae) attacking oaks (Quercus spp.)

Figures 1–3. Psilophrys aristotelei, ♀. (1) Antenna. (2) Fore wing. (3) Ovipositor.

opencc-zeroJul 2023View details →

Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America

Previously unrecognized diseases continue to threaten the health of forest ecosystems globally. Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and within diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two well-supported clades within the genus Lonsdalea, with an average nucleotide identity between them near species boundaries (95.31%) for bacteria, suggesting long isolation. Populations comprise distinct patterns in genetic structure and distribution. Genotypes collected from different host species and habitats were randomly distributed within the California cluster, while most Colorado isolates from introduced planted trees were distinct from isolates collected from a natural stand of CO native Q. gambelii, indicating the presence of cryptic population structure. The distribution of clones in California varied, while Colorado clones were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to migrants moving with nursery stock. Overall results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystem conditions changing. To our knowledge, this is the first study on L. quercina population structure. Further studies are warranted to understand evolutionary relationships among L. quercina populations from different areas, including the native habitat of red oak in northeastern USA.