Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.

Clines in phenotypic traits with an underlying genetic basis potentially implicate natural selection. However, neutral evolutionary processes such as random colonization, spatially restricted gene flow, and genetic drift could also result in similar spatial patterns, especially for single-locus traits because of their susceptibility to stochastic events. One way to distinguish between adaptive and neutral mechanisms is to compare the focal trait to neutral genetic loci to determine whether neutral loci demonstrate clinal variation (consistent with a neutral cline), or not. Ivyleaf morning glory, Ipomoea hederacea, exhibits a latitudinal cline for a Mendelian leaf shape polymorphism in eastern North America, such that lobed genotypes dominate northern populations and heart-shaped genotypes are restricted to southern populations. Here, we evaluate potential evolutionary mechanisms for this cline by first determining the allele frequencies at the leaf shape locus for 77 populations distributed throughout I. hederacea's range and then comparing the geographical pattern at this locus to neutral amplified fragment length polymorphism (AFLP) loci. We detected both significant clinal variation and high genetic differentiation at the leaf shape locus across all populations. In contrast, 99% of the putatively neutral loci do not display clinal variation, and I. hederacea populations show very little overall genetic differentiation, suggesting that there is a moderate level of gene flow. In addition, the leaf shape locus was identified as a major F(ST) outlier experiencing divergent selection, relative to all the AFLP loci. Together, these data strongly suggest that the cline in leaf shape is being maintained by spatially varying natural selection.

Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range.

The presence of substantial genetic variation for water-use efficiency (WUE) suggests that natural selection plays a role in maintaining alleles that affect WUE. Soil water deficit can reduce plant survival, and is likely to impose selection to increase WUE, whereas competition for resources may select for decreased WUE to ensure water acquisition. We tested the fitness consequences of natural allelic variation in a single gene (MPK12) that influences WUE in Arabidopsis, using transgenic lines contrasting in MPK12 alleles, under four treatments; drought/competition, drought/no competition, well-watered/competition, well-watered/no competition. Results revealed an allele × environment interaction: Low WUE plants performed better in competition, resulting from increased resource consumption. Contrastingly, high WUE individuals performed better in no competition, irrespective of water availability, presumably from enhanced water conservation and nitrogen acquisition. Our findings suggest that selection can influence MPK12 evolution, and represents the first assessment of plant fitness resulting from natural allelic variation at a single locus affecting WUE.

Leaf variegation refers to local regions of the upper surface of a leaf having reduced or obstructed chlorophyll, which results in whitish spots. These lighter spots may compromise the photosynthetic efficiency of a leaf, and many competing hypotheses have been put forward to explain why this patterning may be adaptive. It has been suggested that variegation is either an adaptive response to environmental conditions or a defence mechanism against herbivore damage. To test whether leaf variegation reduces herbivore damage, we first assessed the frequency of variegated and nonvariegated leaves in natural populations of the plant Hydrophyllum virginianum L., and second, measured herbivore damage to both variegated and nonvariegated leaves. We found that variegated leaves were present at high frequencies within natural populations (6%–31%) and that nonvariegated leaves sustained nearly twice the amount of damage by comparison with variegated leaves. Therefore, leaf variegation appears to be beneficial by reducing herbivore damage to leaves. These data are consistent with the fundamental prediction of the herbivory hypothesis for the benefits of leaf variegation.

The effect of leaf shape variation on plantherbivore interactions has primarily been studied from the perspective of host seeking behavior. Yet for leaf shape to affect plant-herbivore coevolution, there must be reciprocal effects of leaf shape variation on herbivore consumption and performance. We investigated whether alternative leaf morphs affected the performance of three generalist insect herbivores by taking advantage of a genetic polymorphism and developmental plasticity in leaf shape in the Ivyleaf morning glory, Ipomoea hederacea. Across four experiments, we found variable support for an effect of leaf shape genotype on insects. For cabbage loopers (Trichoplusia ni) and corn earworms (Helicoverpa zea) we found opposing, non-significant trends: T. ni gained more biomass on lobed genotypes, while H. zea gained more biomass on heartshaped genotypes. For army beetworms (Spodoptera exigua), the effects of leaf shape genotype differed depending on the age of the plants and photoperiod of growing conditions. Caterpillars feeding on tissue from older plants (95 days) grown under long day photoperiods had significantly greater consumption, dry biomass, and digestive efficiency on lobed genotypes. In contrast, there were no significant differences between heart-shaped and lobed genotypes for caterpillars feeding on tissue from younger plants (50 days) grown under short day photoperiods. For plants grown under short days, we found that S. exigua consumed significantly less leaf area when feeding on mature leaves than juvenile leaves, regardless of leaf shape genotype. Taken together, our results suggest that the effects of leaf shape variation on insect performance are likely to vary between insect species, growth conditions of the plant, and the developmental stage and age of leaves sampled.

Leaf shape is a highly variable phenotype, and is likely influenced by many sources of selection. Ipomoea hederacea exhibits an adaptive latitudinal cline in leaf shape, which is controlled by a single Mendelian locus: lobed individuals dominate the north with entire-shaped individuals mostly in the south. We test if the following candidate selective agents, suggested by the literature, are responsible for the cline: differential insect herbivory, genetic correlations with other clinal traits like flowering time and growth rate, and thermoregulatory differences. We planted 1680 F 3 individuals, segregating for leaf shape, in the north of I. hederacea's range, where we expected lobed genotypes to have higher fitness. Individuals were assigned to insect removal or control treatments, and we scored herbivory, flowering time, growth rate, leaf temperature, and fitness (seed number). Herbivory, flowering, and growth rate had significant fitness effects, but none differed between leaf shapes. Lobed leaves were consistently warmer at night, but no performance advantage was detected. Finally, we detected no overall fitness differences between leaf shape genotypes, whether we controlled for other traits under selection or not. Our data suggest these candidate selective agents may not be important contributors to the cline, and alternative approaches to understanding the mechanisms maintaining the leaf shape cline in I. hederacea may be necessary.

Disentangling the historical evolutionary processes that contribute to patterns of phenotypic and genetic variation is important for understanding contemporary patterns of both traits of interest and genetic diversity of a species. Ipomoea hederacea is a self-compatible species whose geographic origin is contested, and previous work suggests that although there are signals of adaptation (significant leaf shape and flowering time clines), no population structure or neutral genetic differentiation of I. hederacea populations was detected. Here, we use DNA sequence data to characterize patterns of genetic variation to establish a more detailed understanding of the current and historical processes that may have generated the patterns of genetic variation in this species. We resequenced ca. 5000 bp across 7 genes for 192 individuals taken from 24 populations in North America. Our results indicate that North American I. hederacea populations are ubiquitously genetically depauperate, and patterns of nucleotide diversity are consistent with population expansion. Contrary to previous findings, we discovered significant population subdivision and isolation-by-distance, but genetic structure was spatially discontinuous, potentially implicating long-distance dispersal. We further found significant genetic differentiation at sequenced loci but nearly fourfold stronger differentiation at the leaf shape locus, strengthening evidence that the leaf shape locus is under divergent selection. We propose that North American I. hederacea has experienced a recent founder event, and/or population dynamics are best described by a metapopulation model (high turnover and dispersal), leading to low genetic diversity and a patchy genetic distribution.