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57 results for “Quercus lobata”
Quercus lobata (Fagaceae) - leaf - margin of upper + lower surface
Image of Quercus lobata (Fagaceae) - leaf - margin of upper + lower surface
Data from: Does nutrient scarcity lead to greater variability in seed production? The case of the California valley oak <em>Quercus lobata</em>
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Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations
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Data from: Species diversification in a lineage of Mexican red oak (Quercus section Lobatae subsection Racemiflorae)—the interplay between distance, habitat, and hybridization
In widespread taxa in which hybridization is suspected of being an important aspect of species biology, the patterns and drivers of lineage diversification are not always clear. Here, we examine the patterns of species diversification in a monophyletic lineage of oaks endemic to western Mexico, a center of global oak diversity. This group of four species inhabits a variety of soil types and exhibits varying patterns of species distribution ranging from widespread to restricted, with the range bisected by the Trans-Mexican Volcanic Belt (TVB). Using chloroplast and nuclear microsatellites, we evaluated genetic diversity, diversification, and genetic group assignment across 49 populations. Chloroplast data identified 29 haplotypes in three distinct lineages, many of these found occurring on opposite sides of the TVB. Individual species were only loosely associated to specific chloroplast haplotypes but the distribution of shared haplotypes supports a one-time wider distribution. One lineage was highly divergent and geographically isolated, likely representing a case of chloroplast capture via hybridization and may indicate a range expansion of Racemiflorae into new territory. Nuclear gene diversity varied little across species and populations; however, differentiation and genetic assignment analysis was strongly structured geographically and tended to cluster with broad soil types. Soil specialist taxa produced homogeneous genetic structure while soil generalists showed varying patterns of mixed ancestry and high levels of admixture. Speciation appears driven by a combination of distance and edaphic factors leading to drift. Hybridization appears to be complementary, occurring most often in non-specific soil environments and in marginal areas, and contributes to a long-scale pattern of gene exchange as species ranges fluctuate with time.
Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née
Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.
Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients
DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites or the genes that affect them could be a target of natural selection. Using reduced-representation bisulphite sequencing (RRBS) data, we assessed whether climate is associated with variation in DNA methylation levels among 58 naturally occurring, and species-wide samples of valley oak (Quercus lobata) collected across climate gradients. We identified the genomic context of these variants referencing a new draft valley oak genome sequence. Methylation data were obtained for 341 107 cytosines, of which we deemed 57 488 as single-methylation variants (SMVs), found in the CG, CHG and CHH sequence contexts. Environmental association analyses revealed 43 specific SMVs that are significantly associated with any of four climate variables, the majority of which are associated with mean maximum temperature. The 43 climate-associated SMVs tend to occur in or near genes, several of which have known involvement in plant response to environment. Multivariate analyses show that climate and spatial variables explain more overall variance in CG-SMVs among individuals than in SNPs, CHG-SMVs or CHH-SMVs. Together, these results from natural oak populations provide initial evidence for a role of CG methylation in locally adaptive evolution or plasticity in plant response.
FIGURE 1 in A nomenclatural revision of Quercus acutifolia, Q. conspersa and Q. grahamii (Lobatae, Fagaceae)
FIGURE 1. Variation in the shape of leaves and cup of the acorn of A. Q. acutifolia and B. Q. grahamii.
FIGURE 2. A–G in A new species of Quercus, section Lobatae (Fagaceae) from the Sierra Madre Oriental, Mexico
FIGURE 2. A–G. Some representative leaves of biennial species of Acutifoliae group. A. Quercus meavei; B. Q. grahamii; C. Q. conspersa; D. Q. xalapensis; E. Q. skinneri; F. Q. albocincta; G. Q. uxoris.
FIGURE 1. A–G. Quercus meavei. A in A new species of Quercus, section Lobatae (Fagaceae) from the Sierra Madre Oriental, Mexico
FIGURE 1. A–G. Quercus meavei. A. Branchlet with leaves and fruits; B. Fasciculate trichome from one of the secondary vein axils; C. Fruit; D. Bud; E–G. Variants of leaves.
Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients
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Data from: Species diversification in a lineage of Mexican red oak (Quercus section Lobatae subsection Racemiflorae)—the interplay between distance, habitat, and hybridization
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Data from: Individual resource limitation combined with population-wide pollen availability drives masting in the valley oak (Quercus lobata)
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Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née
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Data from: New approaches to the biogeography and areas of endemism of red oaks (Quercus L., section Lobatae)
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Whole genome bisulfite sequencing for bud, catkin and leaf of California Valley Oak, Quercus lobata (SW786)
GEO Series GSE174826. Quercus lobata. 3 samples. Type: Methylation profiling by high throughput sequencing.
Illumina RNA-seq for bud, leaf and stem of California Valley Oak, Quercus lobata (SW786)
GEO Series GSE174828. Quercus lobata. 3 samples. Type: Expression profiling by high throughput sequencing.
PacBio Iso-Seq transcriptome for California Valley Oak, Quercus lobata (SW786)
GEO Series GSE174827. Quercus lobata. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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