Systems genomics of salinity stress response in rice.

Populations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of ssp.

Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.

Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment.

Systems genomics of salinity stress response in rice.

Populations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of ssp (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions.

Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought.

While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse.

Rapid-cycling Brassica rapa evolves even earlier flowering under experimental drought.

Premise: Changes in climate can impose selection on populations and may lead to rapid evolution. One such climatic stress is drought, which plant populations may respond to with escape (rapid growth and early flowering) or avoidance (slow growth and efficient water-use). However, it is unclear if drought escape would be a viable strategy for populations that already flower early from prior selection.

Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought.

Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations.

Patterns of population genomic diversity in the invasive Japanese knotweed species complex.

Premise: Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity.

Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population.

Background: Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought.

Draining the Swamping Hypothesis: Little Evidence that Gene Flow Reduces Fitness at Range Edges.

The genetic swamping hypothesis proposes that gene flow from central to peripheral populations inhibits local adaptation and is one of the most widely recognized explanations for range limitation. We evaluated empirical support for this hypothesis in studies quantifying patterns of gene flow to peripheral populations and their resulting fitness outcomes. We found little evidence that gene flow is generally asymmetric from central to peripheral populations and also that gene flow tends to have positive effects on edge population fitness.

Climate change alters plant-herbivore interactions.

Plant-herbivore interactions have evolved in response to coevolutionary dynamics, along with selection driven by abiotic conditions. We examine how abiotic factors influence trait expression in both plants and herbivores to evaluate how climate change will alter this long-standing interaction. The paleontological record documents increased herbivory during periods of global warming in the deep past.

Rapid evolutionary changes in gene expression in response to climate fluctuations.

There is now abundant evidence of rapid evolution in natural populations, but the genetic mechanisms of these changes remain unclear. One possible route to rapid evolution is through changes in the expression of genes that influence traits under selection. We examined contemporary evolutionary gene expression changes in plant populations responding to environmental fluctuations.

The strength and pattern of natural selection on gene expression in rice.

Levels of gene expression underpin organismal phenotypes, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown. Here we assayed gene expression in rice (Oryza sativa), and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions.

Evidence for adaptive responses to historic drought across a native plant species range.

As climatic conditions change, species will be forced to move or adapt to avoid extinction. Exacerbated by ongoing climate change, California recently experienced a severe and exceptional drought from 2011 to 2017. To investigate whether an adaptive response occurred during this event, we conducted a "resurrection" study of the cutleaf monkeyflower (), an annual plant, by comparing trait means and variances of ancestral seed collections ("pre-drought") with contemporary descendant collections ("drought").

The influence of environmental factors on breeding system allocation at large spatial scales.

Plant breeding systems can vary widely among populations, yet few studies have investigated abiotic factors contributing to variation across a broad geographic range. Here we investigate variation in reproductive traits of (Campanulaceae), a species that exhibits dimorphic cleistogamy, a condition in which individual plants have both closed (selfing: cleistogamous: CL) and open (selfing or outcrossing: chasmogamous: CH) flowers. Chasmogamous production is theorized to be more costly because CH flowers have a larger exposed surface area and thus are more likely to lose more water than CL flowers.

Two decades of evolutionary changes in Brassica rapa in response to fluctuations in precipitation and severe drought.

As climate changes at unprecedented rates, understanding population responses is a major challenge. Resurrection studies can provide crucial insights into the contemporary evolution of species to climate change. We used a seed collection of two Californian populations of the annual plant Brassica rapa made over two decades of dramatic precipitation fluctuations, including increasingly severe droughts.

Using the resurrection approach to understand contemporary evolution in changing environments.

The resurrection approach of reviving ancestors from stored propagules and comparing them with descendants under common conditions has emerged as a powerful method of detecting and characterizing contemporary evolution. As climatic and other environmental conditions continue to change at a rapid pace, this approach is becoming particularly useful for predicting and monitoring evolutionary responses. We evaluate this approach, explain the advantages and limitations, suggest best practices for implementation, review studies in which this approach has been used, and explore how it can be incorporated into conservation and management efforts.

Phenotypic selection varies with pollination intensity across populations of Sabatia angularis.

Pollinators are considered primary selective agents acting on plant traits, and thus variation in the strength of the plant-pollinator interaction might drive variation in the opportunity for selection and selection intensity across plant populations. Here, we examine whether these critical evolutionary parameters covary with pollination intensity across wild populations of the biennial Sabatia angularis. We quantified pollination intensity in each of nine S.

A harvest of weeds yields insight into a case of contemporary evolution.

When Charles Darwin was exploring the idea of evolution via natural selection, he looked to domesticated species, with the opening chapter of The Origin of Species titled 'Variation Under Domestication' (Darwin ). Domesticated species such as crops are a great example of artificial selection, which Darwin realized was analogous to natural selection. But growing among those carefully selected crop varieties are the unwelcome and unwanted plants we call weeds.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate.

Project Baseline: An unprecedented resource to study plant evolution across space and time.

Premise Of The Study: Project Baseline is a seed bank that offers an unprecedented opportunity to examine spatial and temporal dimensions of microevolution during an era of rapid environmental change. Over the upcoming 50 years, biologists will withdraw genetically representative samples of past populations from this time capsule of seeds and grow them contemporaneously with modern samples to detect any phenotypic and molecular evolution that has occurred during the intervening time.

Methods: We carefully developed this living genome bank using protocols to enhance its experimental value by collecting from multiple populations and species across a broad geographical range in sites that are likely to be preserved into the future.

Predicting the genetic consequences of future climate change: The power of coupling spatial demography, the coalescent, and historical landscape changes.

Premise Of The Study: Climate change is a widely accepted threat to biodiversity. Species distribution models (SDMs) are used to forecast whether and how species distributions may track these changes. Yet, SDMs generally fail to account for genetic and demographic processes, limiting population-level inferences.

Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa.

Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering postdrought, which was previously shown to be adaptive.

Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering.