Quercus Lobata Research Articles

Eco-cultural Restoration of Riparian Wetlands in California: Case Study of White Root (Carex barbarae Dewey; Cyperaceae)

This study defines the cultural and ecological significance of white root (Carex barbarae Dewey; Cyperaceae), and presents a template for eco-cultural restoration, drawing from both Traditional Ecological Knowledge and Scientific Ecological Knowledge. Carex barbarae is an herbaceous perennial understory plant in valley oak riparian woodlands, endemic to California and southern Oregon. Referred to as white root, C. barbarae is an indicator species of both cultural and ecological health. Two-thirds of the California Indian tribes within the range of white root historically tended and managed these sedges for basketweaving. Traditional management by Indian groups resulted in the creation and maintenance of homogeneous patches throughout low-elevation riparian forests of California, maintaining a lawn-like understory and a park-like physiognomy. Gathering and tending practices significantly influenced the distribution, quality and abundance of white root beds on species, community, and landscape scales. Understanding how indigenous people shaped their environment using Traditional Resource Management practices and related ecological effects is integral to successful contemporary restoration of riparian habitats. Understanding the reciprocal relationships between California Indians and their sovereign landscape is important to contemporary indigenous cultures and their identity, resilience, and vitality.

Intraspecific variation in the relationship between weather and masting behavior in valley oak, Quercus lobata

Masting behavior — variable and synchronized reproduction by a population of plants — has long been recognized as correlating with weather. How and why weather conditions influence seed production is, however, poorly understood. We investigated the relationships between acorn production and both local weather and long-term climate in 10 populations across the geographic range of the valley oak (Quercus lobata Née), a California endemic that matures acorns in a single season. Acorn production was larger following a cold spring in the prior year and dry conditions in the winter and spring immediately preceding acorn maturation; similar patterns were also found, with minor differences, at all 10 individual sites. The strength of the relationships varied geographically in the case of the correlation between winter rainfall and annual acorn production, which was stronger (more negative) at wetter sites. Thus, in contrast to a recent study in Quercus petraea (Matt.) Liebl., weather had generally similar effects on acorn production throughout the range of Q. lobata. Similar to Q. petraea, however, the strength of the relationship between site-level annual acorn production and one of the weather factors affecting acorn production (winter rainfall in the case of Q. lobata) varied geographically in ways that may be related to differences among sites in the degree of pollen limitation. Understanding the mechanisms by which weather affects seed production is challenging but critical if we are to understand how climate change will affect masting behavior in the future.

Weather underground: Subsurface hydrologic processes mediate tree vulnerability to extreme climatic drought.

Drought extent and severity have increased and are predicted to continue to increase in many parts of the world. Understanding tree vulnerability to drought at both individual and species levels is key to ongoing forest management and preparation for future transitions in community composition. The influence of subsurface hydrologic processes is particularly important in water-limited ecosystems, and is an under-studied aspect of tree drought vulnerability. With California's 2013-2016 extraordinary drought as a natural experiment, we studied four co-occurring woodland tree species, blue oak (Quercus douglasii), valley oak (Quercus lobata), gray pine (Pinus sabiniana), and California juniper (Juniperus californica), examining drought vulnerability as a function of climate, lithology and hydrology using regional aerial dieback surveys and site-scale field surveys. We found that in addition to climatic drought severity (i.e., rainfall), subsurface processes explained variation in drought vulnerability within and across species at both scales. Regionally for blue oak, severity of dieback was related to the bedrock lithology, with higher mortality on igneous and metamorphic substrates, and to regional reductions in groundwater. At the site scale, access to deep subsurface water, evidenced by stem water stable isotope composition, was related to canopy condition across all species. Along hillslope gradients, channel locations supported similar environments in terms of water stress across a wide climatic gradient, indicating that subsurface hydrology mediates species' experience of drought, and that areas associated with persistent access to subsurface hydrologic resources may provide important refugia at species' xeric range edges. Despite this persistent overall influence of the subsurface environment, individual species showed markedly different response patterns. We argue that hydrologic niche segregation can be a useful lens through which to interpret these differences in vulnerability to climatic drought and climate change.

Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings

Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3–6% absolute reductions and 6.7–43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.

Population ecology and spatial synchrony in the abundance of leaf gall wasps within and among populations of valley oak (Quercus lobata)

AbstractWhat factors drive population variability through space and time? Here we assess patterns of abundance of seven species of gall wasps in three genera occurring on the leaves of valley oaks (Quercus lobata) at 10 sites throughout this species' statewide range in California, from 2000 to 2006. Our primary goals were to understand the factors driving variability in gall abundance and to assess the extent of spatial synchrony in gall wasp communities at both large and small geographic scales. On the large, statewide scale, there was significant site‐to‐site variation in gall abundance, driven in all cases primarily by differences in mean maximum seasonal temperatures, and lesser year‐to‐year variation. In contrast, on the small, local scale, differences were more pronounced from year to year than from tree to tree, and were to some extent correlated with differences in acorn production, suggesting an interaction with the reproductive effort of hosts. Significant spatial synchrony was detected, particularly at the statewide scale, but in no case did synchrony decline significantly with distance, despite sites being up to 741 km apart. Variation in spatial synchrony was correlated with a number of exogenous factors, including seasonal weather conditions, the acorn crop at the statewide scale and soil phosphorus availability at the local scale; however, most variation in spatial synchrony in our analyses remained unexplained.

Urban channel incision and stream flow subsidies have contrasting effects on the water status of riparian trees

The water relations of riparian trees are often closely tied to stream hydrology and channel morphology, which can be altered by urban development. In regions with limited precipitation, urban water use can generate or augment dry-season stream flows, potentially providing a water subsidy to riparian trees. However, urbanization is also associated with high storm flows that cause stream channel incision, or downcutting, which could limit the effect of flow subsidies by lowering riparian water tables. We investigated the effects of urban dry-season flow subsidies and stream channel incision on the water status of streamside trees in Sacramento, California, which has a Mediterranean climate with a distinct and lengthy dry season. For two common facultative riparian species, Quercus lobata (valley oak) and Fraxinus latifolia (Oregon ash), we analyzed both midday stem water potential (Ψstem) measurements and leaf carbon isotope signatures (∂13C) to determine whether channel incision and dry-season flow had interacting effects on seasonal midday water stress and longer-term water use efficiency. We found that stream flow could substantially reduce dry-season water stress in both tree species, but only at low levels of channel incision. Leaf ∂13C signatures for Q. lobata suggested increased water use efficiency in trees growing along incised streams and those lacking dry-season flow. Urban management decisions that affect both dry-season base flows and channel incision can thus influence the growth and health of riparian trees, potentially leading to broader changes in riparian ecosystems.

Artist Statement: The Electrics

Artist StatementThe Electrics Linda Vallejo The Electrics are a fusion of my experiences in the golden days of hippiedom and psychedelic adventures, the magical, hallucinatory quality of indigenous Native American and Mexican ceremonial tradition, and decades spent at the computer manipulating digital imagery. These combined experiences are the basis for my "electrified" paintings and sculptures, where nature and people appear to glow with an almost otherworldly light. The Electrics began as "portraits" of the California Canyon and valley oak which surround my home in Topanga Canyon. For twelve years prior, I had been painting California landscapes in the tradition of fantastic realism, but as I experimented with the oaks they began "morphing" from realism into abstraction. The transition came about when I tried to capture the glow of an oak bathed in the light of a full moon. The painted field became dissected by multiple organic shapes and marks painted in contrary and contrasting colors. Today I have completed several electric oaks, landscapes, and portraits inspired by this first effort where color began to move and vibrate across the canvas. In reading the obituaries recently I have found amazing stories of individuals who have accomplished a great deal and yet are little known. These "unknown heroes" became the basis for a new series entitled Electric Heroes. In asking friends and colleagues for their "list of heroes" I found that many people remembered Gandhi, Martin Luther King, and the Dalai Lama. These renowned figures became the first of my Electric Heroes. My goal now is to complete commissioned head and full body Electric Portraits. In thinking through the artistic process I believe that The Electrics are influenced by Andy Warhol's psychedelic pop icon, the splotchy "pixels" of Chuck Close's portraits, the cosmic 1960s palette and minimal line of Peter Max, and Klimt's emphatic patterning, combined with the visual repetition and coloration of Huichol yarn painting and Indigenous ceremonial bead work. In re-visiting [End Page 214] these artists and their work I am reminded of how the artistic mind "gathers" information and experiences, sometimes over a very long period of time, to reaffirm these influences in the creation of new work. Betty Ann Brown, historian and curator (https://lindavallejo.com/), states: Vallejo's beloved subjects—people and nature—come together in The Electrics, the recent paintings that are expressively energized by vivid color and vibrating form. In this series, the artist has returned to the cosmic vision search initiated in her ceremonially imbued art from the 1980s. The paintings depict the altered state of the sacred that Vallejo experienced in Native American rituals. The Electrics are unified by a brilliant, almost psychedelic palette. From lime green to hot pink, the colors Vallejo chooses recall the intensity and artificiality of early aniline dyes. The paintings are also characterized by consistent calligraphic marks. The tight curls, narrow angles, and parallel hatches all derive from one of the artist's important early experiences. When Vallejo's family lived in Spain, they traveled to the Muslim palace in Granada known as the Alhambra. The young artist was so impressed by the Arabic script used as architectural decoration that she copied it into a notebook—and then repeated the forms again and again. The calligraphy emerges in her early etchings from art school, in later drawings, and now in The Electrics. In the early years of the new millennium, Vallejo began to focus on portraits of single oak trees. I say "portraits" deliberately: these are not generic paintings of plants. Instead they are carefully detailed depictions of individual trees—the wardens and witnesses of Topanga Canyon and other celebrated sites in California, such as Joshua Tree and Boney Ridge. These are fierce and hallucinogenic portrayals of the awesome powers of nature. The growing number of Electric trees and portraits are stunningly beautiful and visionary gifts. [End Page 215] Copyright © 2020 Frontiers Editorial Collective, Inc.

Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow

Climate change over the next century is predicted to cause widespread maladaptation in natural systems. This prediction, as well as many sustainable management and conservation practices, assumes that species are adapted to their current climate. However, this assumption is rarely tested. Using a large-scale common garden experiment combined with genome-wide sequencing, we found that valley oak (Quercus lobata), a foundational tree species in California ecosystems, showed a signature of adaptational lag to temperature, with fastest growth rates occurring at cooler temperatures than populations are currently experiencing. Future warming under realistic emissions scenarios was predicted to lead to further maladaptation to temperature and reduction in growth rates for valley oak. We then identified genotypes predicted to grow relatively fast under warmer temperatures and demonstrated that selecting seed sources based on their genotype has the potential to mitigate predicted negative consequences of future climate warming on growth rates in valley oak. These results illustrate that the belief of local adaptation underlying many management and conservation practices, such as using local seed sources for restoration, may not hold for some species. If contemporary adaptational lag is commonplace, we will need new approaches to help alleviate predicted negative consequences of climate warming on natural systems. We present one such approach, "genome-informed assisted gene flow," which optimally matches individuals to future climates based on genotype-phenotype-environment associations.

Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations.

Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species-wide responses, while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well-watered controls in a common environment by measuring ecophysiological traits in 93 individuals and gene expression (RNA-seq) in 42 individuals. Populations did not differ in their adjustment of turgor loss point during soil drying, suggesting a generalized species-wide response. Differential expression analysis identified 689 genes with a common response to treatment across populations and 470 genes with population-specific responses. Weighted gene co-expression network analysis (WGCNA) identified groups of genes with similar expression patterns that may be regulated together (gene modules). Several gene modules responded differently to water stress among populations, suggesting regional differences in gene network regulation. Populations from sites with a high mean annual temperature responded to the imposed water stress with significantly greater changes in gene module expression, indicating that these populations may be locally adapted to respond to drought. We propose that this variation among valley oak populations provides a mechanism for differential tolerance to the increasingly frequent and severe droughts in California.

Spatio‐temporal variation of biotic and abiotic stress agents determines seedling survival in assisted oak regeneration

Abstract Mediterranean oak woodlands are currently undergoing considerable anthropogenic changes that globally threaten their long‐term persistence. Restoration efforts via assisted regeneration depend on species traits and type of stress. However, how different sources of stress vary across space (microsites) and time (intra‐ and inter‐annual variation) for co‐occurring oak species remains largely unknown. We examined spatio‐temporal variation of biotic (herbivory, seed predation) and abiotic (drought) stress agents to evaluate seedling survival across different regeneration microsites, and considering two climatically contrasting years. We used two co‐occurring species of contrasting ecology and leaf traits in California oak woodlands: the deciduous Quercus lobata (valley oak) and the evergreen Q. agrifolia (coast live oak). Most oak seedlings (98.8%) suffered from some type of stress. For both species, summer drought was the main cause of mortality, followed by rodent damage, ungulate browsing and insect damage. Rodents represented the predominant biotic stress, as all rodent‐affected seedlings eventually died. Interactions among stress factors were nuanced: insect and ungulate‐browsing stresses were greater during dry year, whereas rodent damage was similar in dry and average years. Intra‐annually, rodent damage was the main stress agent in early spring, whereas water stress and ungulate‐browsing were greater from late spring to early fall. Plant species traits were also determinant: overall, the evergreen species had greater survival probability than the deciduous one. Across microsites, water stress showed higher occurrence in open grassland habitats, while rodent damage was prevalent under palatable shrubs and ungulate browsing under conspecific trees. Shrub and tree cover reduced damage attributed to water stress but increased rodent and ungulate damage, respectively. Interestingly, lower water stress but higher rodent damage was found further inside the shrub cover. Synthesis and applications. Intra‐ and inter‐annual variation are critical determinants of stress type and intensity on oak recruitment. Spatial variation (microsite identity) is highly useful to manipulate stress agent impact. We conclude that assisted regeneration should consider not only the predominance and lethality of each stress type and microsite, but also the interactions thereof and thus manipulate protective microsites accordingly.

Historical interactions are predicted to be disrupted under future climate change: The case of lace lichen and valley oak

ABSTRACTAimThe distributions and interactions of co‐occurring species may change if their ranges shift asymmetrically in response to rapid climate change. We aim to test whether two currently interacting taxa, valley oak (Quercus lobata) and lace lichen (Ramalina menziesii), have had a long‐lasting historical association and are likely to continue to associate in the future.LocationCentral western California, western United States of AmericaMethodsUsing population genetic analyses and MaxEnt software for ecological niche modelling, we estimate species’ distributions during the Last Interglacial, the Last Glacial Maximum, present, and future periods. Mantel and vertex (genetic connection) tests were used to examine the spatial congruence among taxa. To compare the modelled response to climate change, we estimated migration speed between respective time periods using vector analysis.ResultsWe found significant genetic congruence between valley oak and the lichen's green algal photobiont, independent of geographic isolation and habitat isolation, which is consistent with long‐term association. Ecological niche models under past and future climate scenarios indicate that overlap of climatic niche sharing between valley oak and lace lichen might decrease in the future. Our models indicate that the speed of shifts in climate niches between these two taxa differed significantly in past periods from that of the present period.Main conclusionsOur findings reveal that historical interactions between valley oak and lace lichen correlate with long‐term sharing of past climate niches. However, the future association of lace lichen with valley oak may be disrupted in parts of its current distribution due to differential discordance of climate niche shifts, species’ movements and generation times. This study illustrates the processes and patterns that allow long‐term association during historic climate change and how they are likely to change during rapid climate change.

Does aggression avoidance drive oak tree attendance by corvid scatter-hoarders?

We investigated the role of species- and community-wide seed production by a community of oaks (Quercus spp.) in influencing tree attendance and aggression among California scrub-jays (Aphelocoma californica), corvids that are seed dispersal mutualists, and acorn woodpeckers (Melanerpes formicivorus), near-exclusive seed predators. We tested the hypothesis that scrub-jays reduce their attendance in response to seed crop size on Quercus lobata, the species preferentially attended by acorn woodpeckers, and therefore reduce the risk of potential injury from aggression when community-level seed production enables them to forage on other trees (the “aggression-avoidance” hypothesis). Results indicated that scrub-jay attendance correlated positively with Q. lobata crops during the year when community-level seed production was low, resulting in high levels of aggression. In contrast, during the 2 years when acorns of other species were abundant in the landscape, scrub-jays reduced attendance at Q. lobata and experienced less aggression. Similarly, we found that the scrub-jays experienced equally low rates of aggression at Q. douglasii trees that were attended by fewer acorn woodpeckers. These results support the aggression-avoidance hypothesis and illustrate how resource and social dynamics may interact to determine the attendance of mutualistic seed dispersers at oak species competing for seed dispersal. Furthermore, they show that intra- and interspecific social interactions at the seed source, as well as at caching locations, affect the scatter-hoarding behavior of wild corvids. SIGNIFICANCE STATEMENT: Food-hoarding animals play a central role in determining the seed fate of large-seeded trees, both in the role of predators and dispersers. Tree attendance and seed hoarding, however, are often context-dependent, varying with population- and community-level seed production, and with intra- and interspecific social dynamics. In California oak communities, acorn woodpeckers—seed predators—compete with California scrub-jays—high-quality seed dispersers—for acorns on preferred trees, resulting in considerable levels of aggression. Using behavioral observations at two species of oaks, one of which is preferred by the woodpeckers, we determined that aggression avoidance explained tree attendance behavior of the scrub-jays, but only when landscape-wide seed production allowed them to forage elsewhere. Our results show for the first time that seed dispersal by hoarding animals can be affected by intra- and interspecific aggression at the seed source.

The importance of native valley oaks (Quercus lobata) as stopover habitat for migratory songbirds in urban Sacramento, California, USA

Urban development occupies over 375,000 ha (6%) of California's Central Valley, and expansion continues to displace natural and agricultural landscapes. The value of urban areas as habitat for native wildlife and the characteristics that determine its value, however, remain little studied. Many Neotropical migrant passerine bird species are declining due to changes in breeding, migratory, and wintering habitats and climatic conditions. During 2010–2013, we evaluated the importance of native valley oak (Quercus lobata) as stopover foraging habitat used by Neotropical migrant birds in urban areas of the Sacramento region in California, USA. Over 3 years, we surveyed spring and late summer-early fall migrant songbirds and measured tree canopy cover within 31 c.0.91 ha transects in Curtis Park, an older residential neighborhood. We detected 607 individuals from 20 migrant species, but four wood warblers comprised the bulk of observations: black-throated gray (Setophaga nigrescens), Wilson's (Cardellina pusilla), orange-crowned (Oreothlypis celata), and yellow warblers (Setophaga petechia). Migrant abundance was closely correlated with valley oak canopy abundance and increased linearly with oak canopy especially during fall migration. Migrants were nearly absent from areas lacking oak canopy. Migrant bird species as a group also foraged in valley oak substantially more often (74%) than would be expected based on its 15% relative canopy cover (χ21d.f. = 924, p < 0.0001), as did all species whose selectivity could be tested. These results are important in demonstrating previously undocumented migrant use of urban areas with remnant valley oak canopy and suggest that protecting existing valley oaks and increasing their use in future urban forestry and landscape plantings in the Central Valley could provide substantial habitat benefits for native migratory birds.

Embryo size as a tolerance trait against seed predation: Contribution of embryo-damaged seeds to plant regeneration

Embryo damage in seed predation is a common occurrence and has been generally considered equivalent to seed death. We hypothesize that seeds with proportionally larger embryos (radicle plus plumule) provide greater tolerance to seed damage by rodents, allowing successful germination. To test this hypothesis, we examined germination and estimated the contribution of embryo-damaged seeds to plant regeneration by comparing the dispersal patterns of intact and embryo-damaged seeds and the ecophysiological responses of their emerged seedlings in two oak species of contrasting embryo size.Our results show that embryo size was positively correlated with seed size in both oak species, but one (Quercus lobata) had proportionally longer embryos than the other (Q. agrifolia), revealing inter-specific differences in embryo size. Probability of embryo excision behavior (partial seed damage to extirpate the embryo) was positively associated with seed size but intensity of damage was relatively constant across all sizes. The species with proportionally longer embryos showed a stronger capacity to regenerate from embryo damage because longer embryos experienced reduced probability of total (lethal) embryo damage by rodents. Seed size and thus intraspecific embryo size only increased germination success in the species with shorter embryos, allowing larger seeds to escape full embryo damage.Seedlings from intact seeds performed better (greater plant biomass and higher chlorophyll and nitrogen index) than those from embryo-damaged seeds. However, seedlings from embryo-damaged seeds showed higher anthocyanin content, a possible response to seed damage. Intact and embryo-damaged acorns showed similar dispersal patterns by rodents (e.g. seed caching behavior and dispersal distances). Importantly, seed retrieval by rodents was significantly lower for embryo-damaged seeds, allowing greater seed survival and supporting the expectation that embryo excision behavior is a strategy to store seeds for longer periods. We conclude that tolerance to embryo damage is an important reproductive strategy that enables plant recruitment. Embryo size could play a crucial role in the evolutionary and ecological responses of seeds to animal predation.

Drivers of synchrony of acorn production in the valley oak (Quercus lobata) at two spatial scales.

We investigated spatial synchrony of acorn production by valley oaks (Quercus lobata) among individual trees at the within-population, local level and at the among-population, statewide level spanning the geographic range of the species. At the local level, the main drivers of spatial synchrony were water availability and flowering phenology of individual trees, while proximity, temperature differences between trees, and genetic similarity failed to explain a significant proportion of variance in spatial synchrony. At the statewide level, annual rainfall was the primary driver, while proximity was significant by itself but not when controlling for rainfall; genetic similarity was again not significant. These results support the hypothesis that environmental factors, the Moran effect, are key drivers of spatial synchrony in acorn production at both small and large geographic scales. The specific environmental factors differed depending on the geographic scale, but were in both cases related to water availability. In addition, flowering phenology, potentially affecting either density-independent pollination failure (the pollination Moran effect) or density-dependent pollination efficiency (pollen coupling), plays a key role in driving spatial synchrony at the local geographic scale.

A New Approach for Interpreting the Morisita Index of Aggregation through Quadrat Size

Spatial point pattern analysis is commonly used in ecology to examine the spatial distribution of individual organisms or events, which may shed light on the operation of underlying ecological processes driving the development of a spatial pattern. Commonly used quadrat-based methods of measuring spatial clustering or dispersion tend to be strongly influenced by the choice of quadrat size and population density. Using valley oak (Quercus lobata) stands at multiple sites, we show that values of the Morisita Index are sensitive to the choice of quadrat size, and that the comparative interpretation of the index for multiple sites or populations is problematic due to differences in scale and clustering intensity from site to site, which may call for different quadrat sizes for each site. We present a new method for analyzing the Morisita Index to estimate the appropriate quadrat size for a given site and to aid interpretation of the clustering index across multiple sites with local differences. By plotting the maximum clustering intensity (Imr) found across a range of quadrat sizes, we were able to describe how a spatial pattern changes when quadrat size varies and to identify scales of clustering and quadrat sizes for analysis of spatial patterns under different local conditions. Computing and plotting the instantaneous rate of change (first derivative of rMax), we were able to evaluate clustering across multiple sites on a standardized scale. The magnitude of the rMax first derivative is a useful tool to quantify the degree of crowding, dispersion, or random spatial distribution as a function of quadrat size.

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus).

The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-sited associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of de novo assembly versus assembly by mapping to a reference genome. Using RADseq data for 83 oak samples representing 16 taxa, we identified variants via three pipelines: mapping sequence reads to a recently published draft genome of Quercus lobata, and de novo assembly under two sets of locus filters. For each pipeline, we inferred the maximum likelihood phylogeny. All pipelines produced similar trees, with minor shifts in relationships within well-supported clades, despite the fact that they yielded different numbers of loci (68 000 - 111 000 loci) and different degrees of overlap with the reference genome. We conclude that both the reference-aligned and de novo assembly pipelines yield reliable results, and that advantages and disadvantages of these approaches pertain mainly to downstream uses of RADseq data, not to phylogenetic inference per se.

Spatial Clustering and Ecological Crowding of Valley Oak (Quercus lobata, Née) Associated with Shifts in Recruitment Establishment Sites in Southern California

Premise of research. Valley oak (Quercus lobata, Nee) has received much attention due to concerns about regeneration failure and, more recently, compositional and structural community changes associated with this foundation species. Changes in the structure and spatial distribution of valley oak stands, as examined in this article, are likely affecting ecological processes and interactions throughout communities where it is found.Methodology. We used quadrat-based methods of spatial analysis, Morisita’s index of aggregation (IM), and a derived index (IMr) to examine patterns of clustering, intensity of crowding, and changes in the probability of crowding as the definition of crowding (stems/area) is changed. Saplings, defined as stems with a diameter at breast height (dbh) greater than 1 cm and less than 10 cm (1 cm ≤ dbh < 10 cm) and adults (dbh ≥ 10 cm) were analyzed using four quadrat sizes. We mapped clusters of stems on the basis of spatial autocorrelation of dbh using Anselin’s local Moran’s I to id...

Effects of landscape features on gene flow of valley oaks (Quercus lobata)

Landscape features affect habitat connectivity and patterns of gene flow and hence influence genetic structure among populations. We studied valley oak (Quercus lobata), a threatened species of California (USA) savannas and oak woodlands, with a distribution forming a ring around the Central Valley grasslands. Our main goal was to determine the role of topography and land cover on patterns of gene flow and to test whether elevation or land cover forms stronger barriers to gene flow among valley oak populations. We sampled valley oaks in 12 populations across the range of this species, genotyped each tree at eight nuclear microsatellite loci, and created a series of resistance surfaces by assigning different resistance values to land cover type and elevation. We also estimated recent migration rates and evaluated them with regard to landscape features. There was a significant but weak relationship between Euclidian distance and genetic distance. There was no relationship between genetic distances and land cover, but a significant relationship between genetic distances and elevation resistance. We conclude that gene flow is restricted by high elevations in the northern part of the valley oak range and by high elevations and the Central Valley further south. Migration rate analysis indicated some gene flow occurring east–west but we suggest that the high connectivity in the northern Central Valley is facilitating the formation of these links. We predict that southern populations may become more differentiated in the future through genetic isolation and local adaptation taking place in the face of climate change.

Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata.

Reduced water availability during drought can create major stress for many plant species. Within a species, populations with a history of seasonal drought may have evolved the ability to tolerate drought more than those in areas of high precipitation and low seasonality. In this study, we assessed response to water stress in a California oak species, Quercus lobata Née, by measuring changes in gene expression profiles before and after a simulated drought stress treatment through water deprivation of seedlings in a greenhouse setting. Using whole-transcriptome sequencing from nine samples from three collection localities, we identified which genes are involved in response to drought stress and tested the hypothesis that seedlings sampled from climatically different regions of the species range respond to water stress differently. We observed a surprisingly massive transcriptional response to drought: 35,347 of 68,434 contigs (52%) were differentially expressed before versus after drought treatment, of which 18,111 were down-regulated and 17,236 were up-regulated. Genes functionally associated with abiotic stresses and death were enriched among the up-regulated genes, whereas metabolic and cell part-related genes were enriched among the down-regulated. We found 56 contigs that exhibited significantly different expression responses to the drought treatment among the three populations (treatment × population interaction), suggesting that those genes may be involved in local adaptation to drought stress. These genes have stress response (e.g., WRKY DNA-binding protein 51 and HSP20-like chaperones superfamily protein), metabolic (e.g., phosphoglycerate kinase and protein kinase superfamily protein), transport/transfer (e.g., cationic amino acid transporter 7 and K+ transporter) and regulatory functions (e.g., WRKY51 and Homeodomain-like transcriptional regulator). Baseline expression levels of 1310 unique contigs also differed among pairs of populations, and they were enriched for metabolic and cell part-related genes. Out of the large fraction of the transcriptome that was differentially expressed in response to our drought treatment, we identified several novel genes that are candidates for involvement in local adaptation to drought.