Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis

Experimental test of the contributions of initial variation and new mutations to adaptive evolution in a novel environment

Experimental evolution is an approach that allows researchers to study organisms as they evolve in controlled environments. Despite the growing popularity of this approach, there are conceptual gaps among projects that use different experimental designs. One such gap concerns the contributions to adaptation of genetic variation present at the start of an experiment and that of new mutations that arise during an experiment. The primary source of genetic variation has historically depended largely on the study organisms. In the long-term evolution experiment (LTEE) using Escherichia coli, for example, each population started from a single haploid cell, and therefore, adaptation depended entirely on new mutations. Most other microbial evolution experiments have followed the same strategy. By contrast, evolution experiments using multicellular, sexually reproducing organisms typically start with preexisting variation that fuels the response to selection. New mutations may also come into play in later generations of these experiments, but it is generally difficult to quantify their contribution in these studies. Here, we performed an experiment using E. coli to compare the contributions of initial genetic variation and new mutations to adaptation in a new environment. Our experiment had four treatments that varied in their starting diversity, with 18 populations in each treatment. One treatment depended entirely on new mutations, while the other three began with mixtures of clones, whole-population samples, or mixtures of whole-population samples from the LTEE. We tracked a genetic marker associated with different founders in two treatments. These data revealed significant variation in fitness among the founders, and that variation impacted evolution in the early generations of our experiment. However, there were no differences in fitness among the treatments after 500 or 2,000 generations in the new environment, despite the variation in fitness among the founders. These results indicate that new mutations quickly dominated, and eventually they contributed more to adaptation than did the initial variation. Our study thus shows that preexisting genetic variation can have a strong impact on early evolution in a new environment, but new beneficial mutations may contribute more to later evolution and can even drive some initially beneficial variants to extinction.

Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed

In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.

The molecular bases of floral scent evolution under artificial selection: insights from a transcriptome analysis in Brassica rapa

In an artificial selection experiment using fast-cycling Brassica rapa plants it was recently shown that floral VOCs respond rapidly to selection for increased amounts. Here we carried out transcriptome analysis in these plants to explore the molecular bases of the augmentation in the artificially selected scent compound, phenylacetaldehyde (PAA), as well as other compounds that increased through pleiotropy. In the transcriptome data, we found up-regulation of genes likely underlying PAA synthesis, but also several genes of the shikimate pathway and the related phenylalanine metabolism. As phenylalanine is the precursor of many aromatic volatiles that showed increased emission, this result could explain some of the pleiotropic evolutionary responses. In addition, we found that ribosomal protein genes were up-regulated in “high” (high PAA amount) selection line plants, a mechanism that might further augment the effect of elevated gene expression at the proteomic level. Our study shows that selection on an individual trait can impose changes in the expression of several different genes, which could explain pleiotropic responses in the biosynthetic network of floral volatiles.

Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

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. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus

The influence of genetic interactions (epistasis) on the genetic variance of quantitative traits is a major unresolved problem relevant to medical, agricultural, and evolutionary genetics. The additive genetic component is typically a high proportion of the total genetic variance in quantitative traits, despite that underlying genes must interact to determine phenotype. This study estimates direct and interaction effects for 11 pairs of Quantitative Trait Loci (QTLs) affecting floral traits within a single population of Mimulus guttatus. With estimates of all 9 genotypes for each QTL pair, we are able to map from QTL effects to variance components as a function of population allele frequencies, and thus predict changes in variance components as allele frequencies change. This mapping requires an analytical framework that properly accounts for bias introduced by estimation errors. We find that even with abundant interactions between QTLs, most of the genetic variance is likely to be additive. However, the strong dependency of allelic average effects on genetic background implies that epistasis is a major determinant of the additive genetic variance, and thus, the population’s ability to respond to selection.

Complex traits are influenced not only by the effects of individual genes but also by the myriad ways that these genes interact with one another, commonly referred to as epistasis. Theory suggests that epistasis could have important population-level implications in terms of the genetic variance components that govern evolution in response to natural or artificial selection. Unfortunately, empirical examples extending from observed interactions between genes to genetic variances are scant, particularly for natural populations. Here, we characterize epistasis between naturally segregating polymorphisms in M. guttatus and determine the cumulative effect of epistasis on population genetic variance components. To do this, we first elaborate the necessary statistical theory to accommodate estimation error in genetic effects, as failing to do so will upwardly bias variance predictions. We find that gene interactions have a net positive effect on both the total and additive genetic variance for most traits; however, the contribution of individual loci to the additive variance depends heavily on the genotype frequencies at other loci. Therefore, the effect of epistasis extends beyond the individual’s phenotype to influence how both populations and their component alleles respond to selection.

Major QTLs for critical photoperiod and vernalization underlie extensive variation in flowering in the Mimulus guttatus species complex

Species with extensive ranges experience highly variable environments with respect to temperature, light and soil moisture. Synchronizing the transition from vegetative to floral growth is important to employ favorable conditions for reproduction. Optimal timing of this transition might be different for semelparous annual plants and iteroparous perennial plants. We studied variation in the critical photoperiod necessary for floral induction and the requirement for a period of cold-chilling (vernalization) in 46 populations of annuals and perennials in the Mimulus guttatus species complex. We then examined critical photoperiod and vernalization QTLs in growth chambers using F(2) progeny from annual and perennial parents that differed in their requirements for flowering. We identify extensive variation in critical photoperiod, with most annual populations requiring substantially shorter day lengths to initiate flowering than perennial populations. We discover a novel type of vernalization requirement in perennial populations that is contingent on plants experiencing short days first. QTL analyses identify two large-effect QTLs which influence critical photoperiod. In two separate vernalization experiments we discover each set of crosses contain different large-effect QTLs for vernalization. Mimulus guttatus harbors extensive variation in critical photoperiod and vernalization that may be a consequence of local adaptation.

Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella

Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species’ range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago.

Mapping the genetic basis of ecologically and evolutionarily relevant traits in Arabidopsis thaliana

There has been a long standing interest in the relationship between genetic and phenotypic variation in natural populations, in order to understand the genetic basis of adaptation and to discover natural alleles to improve crops. Here we review recent developments in mapping approaches that have significantly improved our ability to identify causal polymorphism explaining natural variation in ecological and evolutionarily relevant traits. However, challenges in interpreting these discoveries remain. In particular, we need more detailed transcriptomic, epigenomic, and gene network data to help understand the mechanisms behind identified associations. Also, more studies need to be performed under field conditions or using experimental evolution to determine whether polymorphisms identified in the lab are relevant for adaptation and improvement under natural conditions.

Correlated response in plasticity to selection for early flowering in Arabidopsis thaliana

Phenotypic plasticity is an important strategy for coping with changing environments. However, environmental change usually results in strong directional selection, and little is known empirically about how this affects plasticity. If genes affecting a trait value also affect its plasticity, selection on the trait should influence plasticity. Synthetic outbred populations of Arabidopsis thaliana were selected for earlier flowering under simulated spring- and winter-annual conditions to investigate the correlated response of flowering time plasticity and its effect on family-by-environment variance (Vg×e) within each selected line. We found that selection affected plasticity in an environmentally dependent manner: under simulated spring-annual conditions, selection increased the magnitude of plastic response but decreased Vg×e; selection under simulated winter-annual conditions reduced the magnitude of plastic response but did not alter Vg×e significantly. As selection may constrain future response to environmental change, the environment for crop breeding and ex situ conservation programmes should be carefully chosen. Models of species persistence under environmental change should also consider the interaction between selection and plasticity.

Local selection across a latitudinal gradient shapes nucleotide diversity in balsam poplar, Populus balsamifera L

Molecular studies of adaptive evolution often focus on detecting selective sweeps driven by positive selection on a species-wide scale; however, much adaptation is local, particularly of ecologically important traits. Here, we look for evidence of range-wide and local adaptation at candidate genes for adaptive phenology in balsam poplar, Populus balsamifera, a widespread forest tree whose range extends across environmental gradients of photoperiod and growing season length. We examined nucleotide diversity of 27 poplar homologs of the flowering-time network-a group of genes that control plant developmental phenology through interactions with environmental cues such as photoperiod and temperature. Only one gene, ZTL2, showed evidence of reduced diversity and an excess of fixed replacement sites, consistent with a species-wide selective sweep. Two other genes, LFY and FRI, harbored high levels of nucleotide diversity and exhibited elevated differentiation between northern and southern accessions, suggesting local adaptation along a latitudinal gradient. Interestingly, FRI has also been identified as a target of local selection between northern and southern accessions of Arabidopsis thaliana, indicating that this gene may be commonly involved in ecological adaptation in distantly related species. Our findings suggest an important role for local selection shaping molecular diversity and reveal limitations of inferring molecular adaptation from analyses designed only to detect species-wide selective sweeps.

Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana

Flowering time (FT) is the developmental transition coupling an internal genetic program with external local and seasonal climate cues. The genetic loci sensitive to predictable environmental signals underlie local adaptation. We dissected natural variation in FT across a new global diversity set of 473 unique accessions, with >12,000 plants across two seasonal plantings in each of two simulated local climates, Spain and Sweden. Genome-wide association mapping was carried out with 213,497 SNPs. A total of 12 FT candidate quantitative trait loci (QTL) were fine-mapped in two independent studies, including 4 located within ±10 kb of previously cloned FT alleles and 8 novel loci. All QTL show sensitivity to planting season and/or simulated location in a multi-QTL mixed model. Alleles at four QTL were significantly correlated with latitude of origin, implying past selection for faster flowering in southern locations. Finally, maximum seed yield was observed at an optimal FT unique to each season and location, with four FT QTL directly controlling yield. Our results suggest that these major, environmentally sensitive FT QTL play an important role in spatial and temporal adaptation.

Genetic and physiological bases for phenological responses to current and predicted climates

We are now reaching the stage at which specific genetic factors with known physiological effects can be tied directly and quantitatively to variation in phenology. With such a mechanistic understanding, scientists can better predict phenological responses to novel seasonal climates. Using the widespread model species Arabidopsis thaliana, we explore how variation in different genetic pathways can be linked to phenology and life-history variation across geographical regions and seasons. We show that the expression of phenological traits including flowering depends critically on the growth season, and we outline an integrated life-history approach to phenology in which the timing of later life-history events can be contingent on the environmental cues regulating earlier life stages. As flowering time in many plants is determined by the integration of multiple environmentally sensitive gene pathways, the novel combinations of important seasonal cues in projected future climates will alter how phenology responds to variation in the flowering time gene network with important consequences for plant life history. We discuss how phenology models in other systems--both natural and agricultural--could employ a similar framework to explore the potential contribution of genetic variation to the physiological integration of cues determining phenology.

Seasonal and developmental timing of flowering

The coordination of the timing of flowering with seasonal and development cues is a critical life-history trait that has been shaped by evolution to maximize reproductive success. Decades of studying many plant species have revealed several of the fascinating systems that plants have evolved to control flowering time: such as the perception of day length in leaves, which leads to the production of a mobile signal, florigen, that promotes flowering at the shoot apical meristem; the vernalization process in which exposure to prolonged cold results in meristem competence to flower; and the juvenile to adult phase transition. Arabidopsis research has contributed greatly to understanding these systems at a molecular level.

Seasonal flowering and evolution: the heritage from Charles Darwin

To survive, plants optimise their seasonal flowering time and set seed to avoid extremes of the environment including frost, heat and drought. Additionally, pollination may need to be tightly regulated in time so that it coincides with flowering of other individuals and/or with the presence of bird or insect pollinators. It is now clear that plants use seasonal changes in natural light intensity, daylight duration and temperature to achieve reproducible timing of flowering year-in-year-out. In more recent studies, genetic and molecular approaches are beginning to provide a basis for understanding heritability, an essential component of Darwin's concept of evolution.

Pleiotropic effects of environment-specific adaptation in Arabidopsis thaliana

Local adaptation may be important for the preservation of genetic diversity and the promotion of speciation. However, local adaptation may also constrain establishment in different environments. The consequences of local adaptation depend strongly on the pleiotropic effects of the genes involved in adaptation. Here, we investigated the pleiotropic effects of the genetic response to selection in outbred lines of Arabidopsis artificially selected to flower earlier under both winter- and spring-annual simulated conditions. The consequences of adaptation were evaluated by reciprocally transplanting selected and control lines between the two conditions. Selected lines always flower earlier than their controls, independent of growing conditions. However, selected lines, growing in the same condition in which they were selected, flower earlier than plants selected in the alternative environment. Plants selected to flower earlier in spring produce more fruits than controls when growing in the spring, and less fruits when growing in the winter; indicating that local adaptation has negative pleiotropic effects in another environment. Our results indicate that local adaptation can arise even when selection targets the same trait in the same direction. Furthermore, it suggests that adaptation under the two different environments can generate fitness trade-offs that can maintain genetic variation for flowering time.