152 research outputs found
MicrosatelliteData
No full textData generated at Victoria Sork Lab, University of California Los Angeles (UCLA). This file contains the genotypes for 9 microsatellite loci and 128 individuals collected in 20 populations of Engelmann oak (Quercus engelmannii
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Ecological Processes and Genomic Variation Associated with Seedling Performance in Tropical and Temperate Trees
No full textUnderstanding the response of plants to natural selection is an important topic in plant evolutionary ecology, both in terms of understanding what structures plant populations spatially and genetically and how plants will be able to respond to changing conditions. We investigate three means by which seedlings respond to selection pressure: spatial escape, evolutionary response via local adaptation, and phenotypically plastic responses measured as changes in gene expression. First, in tropical forest in Ecuador, we test the classic Janzen-Connell hypothesis that seed dispersal is advantageous because it provides escape from host-specific soil pathogens associated with high seedling densities near maternal trees. In support of this hypothesis, we find that survival of Pentagonia macrophylla seedlings in the field increases and disease incidence decreases with decreasing density of conspecifics of various life stages. However, a greenhouse experiment suggests that trade-offs between dispersal and local adaptation, along with spatial heterogeneity in soil properties, shape seedling establishment. Second, we propose a method to test for evidence of selection in seedling populations, using two oak species (Quercus douglasii and Q. kellogii) planted in common gardens in California as case studies. We test for genetic differentiation between multivariate genotypes of seedling populations that survive or die and find that selection acts more strongly at distant than local sites and that the signal of selection increases over time. Employing SNP-survival association tests, we further identify 31 variants that may be responsible for observed genetic divergence between seedlings that lived versus died. Finally, we test the effects of one pervasive selective pressure, drought stress, on variation in gene expression among seedlings within a population of Q. douglasii seedlings. We identify a suite of genes that consistently respond to drought stress across all maternal families tested, in addition to a set of 70 genes whose transcriptional response to drought varies with family, providing adaptive potential to respond to changing conditions. This work suggests that selection by pathogens shapes the spatial structure of a tropical tree population and that standing variation in a temperate tree population may allow adaptive evolutionary and plastic responses to changing climate
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Evidence of Hybridization and Introgression in Two Distantly Related, Sympatric Californian White Oaks (Quercus sect. Quercus)
No full textClimate regimes are changing rapidly at a global scale and the rate of change often outpaces the ability of many species to evolve in response to changing selective pressures. It is possible that other evolutionary processes, such as introgressive hybridization, allow species to exchange alleles across species boundaries at rates that exceed the creation of novel adaptive alleles through mutation alone. By analyzing genomic sequence data for evidence of ancient adaptive introgression, we can characterize the role that this process played in the evolutionary history of these species and its potential under predicted future climate regimes. Here, we test for evidence of adaptive introgression in two hybridizing white oaks (Quercus sect. Quercus): the drought tolerant California shrub oak (Quercus berberidifolia) and the comparatively drought intolerant tree Engelmann oak (Quercus engelmannii). In Chapter 1, we use single nucleotide polymorphisms (SNPs) generated by reduced-representation sequencing to test the likelihood of various ancient demographic models to identify the presence, timing, and direction of ancient introgression in this system. We discovered evidence of asymmetric introgression from Q. berberidifolia during the advent of a Mediterranean-type climate, indicating a potential association between ancient gene flow between these species and large-scale climatic change.
In Chapter 2 we used whole genome sequence data to characterize landscape-scale distribution of genetic diversity in both Q. engelmannii and Q. berberidifolia. We also identified and compared candidate SNPs significantly associated with climatic gradients to neutral genetic diversity under current and future predicted climate models. Evidence showed that Q. engelmannii is likely well-adapted to current local climate conditions throughout its range and is more likely to become maladapted under future climate scenarios.
In Chapter 3 we test for evidence of introgression in both species and identified any functional genes found in physical regions of introgression. We discovered significant genome-wide evidence of introgression of functional genes associated with stress response in Q. engelmannii but did not find any significant evidence of introgression in Q. berberidifolia. This combined evidence suggests that ancient adaptive introgression with Q. berberidifolia may have allowed Q. engelmannii to adapt to past large-scale climate change
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Local climatic heterogeneity predicts differences in phenotypic plasticity across populations of a widely-distributed California oak species
No full textIn variable environments, phenotypic plasticity-- the ability of a genotype to produce different phenotypes in different environments -- may play a critical role in survival of an organism. It has been proposed that populations living in more climatically variable environments may evolve greater phenotypic plasticity than populations in more stable environments, which may be particularly beneficial for sessile long-lived organisms, such as trees, which once established will live in one location for a long time. We test this hypothesis by examining leaf traits in Quercus lobata, a wide-spread California oak, which were planted into two common gardens. Common gardens were established with 6000 seedlings grown from acorns harvested from trees across the species range. We measure leaf traits that are likely to demonstrate plasticity, and are known to be associated with plant response to climate. In support of our hypothesis, we find that leaf thickness, leaf lobedness, and trichome density show clines in plasticity in their response to the environments of the two gardens that are correlated with two measures of environmental heterogeneity—temperature seasonality and precipitation seasonality. Seedlings from climates which are more seasonal in temperature and precipitation tend to display higher levels of plasticity in the common gardens. We also find geographic structure in patterns of plasticity and identify leaf lobedness as the most plastic leaf trait in the common gardens. More plastic maternal families tend to display lower levels of fitness in the common gardens suggesting a cost associated with plasticity. We conclude that there is local adaptation for plasticity in some leaf traits, and that there is a fitness cost to that plasticity outside of the native environment
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Bat pollination, genetic structure and gene flow in Crescentia alata trees in Westrn Mexico
No full textBats are important pollinators of flowering trees in the tropics. Tropical forests are facing increasing threats from fragmentation, but it is unclear how this affects pollinators, or gene flow in bat-pollinated trees. The goals of this dissertation are to evaluate the impact of forest fragmentation on the abundance of pollinating bats, the reproductive success of trees, and contemporary pollen flow in a bat-pollinated tropical tree species, Crescentia alata. We also describe the genetic structure of this plant species, to better understand if the loss of its theorized seed disperser in the Pleistocene has caused restricted seed dispersal. To assess the impact of forest fragmentation, we sampled bat pollinator abundance and seedling genotypes in sites in continuous and fragmented forest, in the area of the Chamela-Cuixmala Biosphere Reserve, in Jalisco, México. We also sampled adult trees at a slightly larger geographic scale. We developed neutral molecular markers for this species and employed spatial genetic structure analyses to understand gene flow patterns. We hypothesized that adult populations of Crescentia alata have high genetic structuring due to the loss of its seed disperser, but that seedlings will show low pollen pool genetic structure, resulting from high gene flow from the long distance foraging movements of bats. We found evidence that bat abundance is a function of floral display, and seems unaffected by forest fragmentation around flowering trees. Fruit-set was higher in fragmented forest sites, as was pollen flow, although the majority of diversity was found at the level of fruit, rather than at the level of site (sub-population).There was little evidence for restricted seed dispersal among adults, which may be due to high pollen flow or seed dispersal by seasonal floods. These findings contradict the idea that pollen flow is reduced by forest fragmentation, and suggest that bats are moving pollen widely across the landscape, and carrying genetically diverse pollen loads to each flower. These results highlight the important role bat pollinators play in maintaining genetic connectivity among plant populations
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The population biology of dispersal and gene flow in the desert shrub Acacia (Senegalia) greggii A. Gray in the Mojave National Preserve
No full textDesert ecosystems are increasingly affected by the human-driven environmental pressures currently changing global landscapes and climates. Plant species are especially susceptible to these changes due to their inability to move except through propagules and a frequent reproductive dependence on dispersing animal species that could themselves be displaced. To identify the limitations climate and landscape already exert on the movement and reproduction of plant species in desert zones, we examined the desert shrub Acacia (Senegalia) greggii A. Gray in the Mojave National Preserve. In chapter one, we give an overview of the ecosystem and study species. In chapter two, we present determinants of reproductive success in A. greggii shrubs. Limited water availability in deserts leads to annual and spatial variation in floral production. The impact of this variation on the reproductive success of a plant depends on the response of dispersal agents and seed predators to fluctuating food resources. We conducted observational surveys and experimental manipulations, and found that greater floral abundance attracted a greater number of pollinators, increased fruit-set, decreased the seed predation rate, and thus increased the pre-dispersal reproductive success of the shrub. In chapter three we present the historic and contemporary dispersal in A. greggii. We compared the genetic patterns of adults and pollen in a 4 km2 area, and found widespread gene flow indicating pollen flow may be more extensive than seed dispersal. Despite this extensive movement, both adult and pollen genetic patterns were explained by separation between dry-washes, suggesting a potential dispersal corridor for pollen and seeds. In chapter four, we present our comparison of alternative landscape pathways derived from both climatic and topographic variables to explain regional genetic structure. We examined movement across 2,700 km2 to determine if the fine-scale patterns observed in chapter three translate into regional connectivity. We again found widespread dispersal was best explained by gene flow along dry-washes. Our work documents a species with a well-adapted reproductive strategy and historically widespread dispersal. In spite of these results, the movement pattern of A. greggii is shaped by landscape features suggesting a potential impact of landscape change and development on future movement
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Comparing phenotypic and genetic variation in California walnuts (Juglans californica and J. hindsii) to resolve species identities and scan for climate adaptations
No full textJuglans californica and J. hindsii are sister taxa endemic to California with significant economic, ecological, and cultural relevance to the state. Each taxon is a foundation species for a rare and threatened plant community, the walnut woodland, in their respective regions. Both species are distributed throughout much of California, but their species identities still need clarification due to some authorities' treatment of both taxa as subspecies of Juglans californica. The future of either taxon will need to confront climate change within a highly urbanized and fragmented landscape, where the usual options for long-living tree species are to adapt, disperse, or die, but landscape genomic-based predictions cannot occur without a clear understanding of how each taxon is genetically and ecologically distinct. Using herbarium specimens and whole-genome sequences for 104 field-identified Juglans californica sampled throughout California, we describe spatially explicit patterns of leaf morphology, genetic structure, and genetic diversity in both taxa and leverage genetic-environment associations to describe distinct patterns of local adaptation that corroborate that these taxa are should be treated as different species. Genetic structure analyses suggest that J. californica is restricted to the Los Angeles Metropolitan area and the Transverse Ranges. J. hindsii occurs throughout much of Northern California and extends into the southmost portion of the species range in San Diego County. Hybridization with a third cluster occurs throughout both of the species. Leaf trait values, including abaxial vein axil hair area, leaflet number, and petiole length, significantly differ between species and corroborate genetic structure results. J. hindsii has higher genetic diversity than J. californica (nucleotide diversity, biallelic richness, and observed heterozygosity) and local adaptation patterns strongly influenced by winter bioclimatic variables based on GEA analyses. J. californica has local adaptation patterns that are strongly influenced by summer temperature and water availability. These results suggest that each species may respond differently to climate change projections and require species-specific protections against ongoing habitat loss and climate change
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Evolution and drought adaptation of California oaks across and within species
No full textPlants have evolved to survive a wide range of environmental stressors. Current climate change models predict higher frequency and severity of California droughts. It is imperative to understand the impact that stress has on plant performance to predict changes in habitat distributions and abundance for all plants species. While most work examines broad scales across multiple genera, few studies analyze plant drought tolerance within a single genera or species. The highly diverse woody genus, Quercus (oaks), contains ~450 long-lived woody species that dominate the Northern Hemisphere, and now faces threats from climate change. My research explores gaps in plant-hydraulic theory by comparing key drought tolerance traits – minimum leaf surface conductance (gmin), stomatal conductance (gs) and leaf hydraulic conductance (Kleaf) – to climate variables, in closely related California Quercus species grown in a common garden. I show that gmin is driven by cuticle layer permeability and stomatal aperture. Furthermore, I found that native California oaks reduce their hydraulic capacity before stomata are fully closed to prevent water loss. I expanded on this work to explore the morphological and physiological leaf traits within a single species, Quercus lobata, grown in two common gardens. Valley oaks show local adaptation to their climate, with many of their physical traits being shaped by climate-driven selection. Morphological traits are more influenced by genetics, while ecophysiological traits are more adaptable to environmental changes. Some traits vary significantly among different oak families, and these differences are linked to the climate conditions of their maternal origins, indicating that the climate where the mother tree grew influences these traits. Lastly, I investigated biomass and nutrient allocation trade-offs in Q. lobata by analyzing above- and belowground biomass and carbon and nitrogen concentrations in juvenile trees. Valley oak families show plasticity in their root-to-shoot ratios and some nutrient traits when grown in common gardens, aligning with previous studies on resource allocation. However, genetic differentiation and climate selection were found in various biomass traits, but not in root-to-shoot ratios or nutrient traits. Overall, Valley oak uses a mixed strategy to adapt to climate conditions. Collectively, this research underscores the importance of studying plant drought tolerance, at both the genus and species levels, by seeking to clarify environmental drivers of oak trait responses
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