Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance.

The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed.

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory.

Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field, and paired this work with an examination of gene expression changes. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to nonselected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs. outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed.

The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.

The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed.

Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift, and selection. Here, we use genome-wide molecular markers to characterize the population genetic structure and connectivity of Ipomoea purpurea (Convolvulaceae), a noxious invasive weed. We, likewise, assess the interaction between natural and human-driven influences on genetic differentiation among populations. Our analyses find that human population density is an important predictor of pairwise population differentiation, suggesting that the agricultural and/or horticultural trade may be involved in maintaining some level of connectivity across distant agricultural fields. Climatic variation appears as an additional predictor of genetic connectivity in this species. We discuss the implications of these results and highlight future research needed to disentangle the mechanistic processes underlying population connectivity of weeds.

Microsatellite markers for Corybas (Orchidaceae) species in New Zealand.

PREMISE OF THE STUDY: Microsatellite markers were developed for New Zealand species of Corybas (Orchidaceae) to investigate population genetics and species delimitation. METHODS AND RESULTS: From sequencing a total genomic DNA library (using Illumina MiSeq), we developed 22 microsatellite markers for C. obscurus. The di- and trinucleotide repeat loci were initially trialed on individuals representing seven Corybas taxa (C. "rimutaka," C. confusus, C. hypogaeus, C. macranthus, C. obscurus, C. trilobus, and C. walliae) and had one to eight alleles per locus. Twelve polymorphic markers were further tested on six Corybas populations from three of the seven taxa (C. obscurus, C. "rimutaka," and C. trilobus). Observed and expected heterozygosities ranged from 0-1 and 0-0.859, respectively. The utility of these 12 loci was further validated in five related Corybas species (C. hypogaeus, C. obscurus, C. vitreus, C. walliae, and C. "rimutaka"; 38 individuals) representing populations from across the North and South Islands. The average value for genetic diversity among populations (F ST) of 0.439 shows differentiation among species. CONCLUSIONS: These markers will be useful for future studies aimed at delimiting species boundaries and examining the genetic diversity of the New Zealand Corybas species.

Not all weeds are created equal: A database approach uncovers differences in the sexual system of native and introduced weeds.

Weedy species provide excellent opportunities to examine the process of successful colonization of novel environments. Despite the influence of the sexual system on a variety of processes from reproduction to genetic structure, how the sexual system of species influences weediness has received only limited consideration. We examined the hypothesis that weedy plants have an increased likelihood of being self-compatible compared with nonweedy plants; this hypothesis is derived from Baker's law, which states that species that can reproduce uniparentally are more likely to successfully establish in a new habitat where mates are lacking. We combined a database of the weed (weedy/nonweedy) and introduction status (introduced/native) of plant species found in the USA with a database of plant sexual systems and determined whether native and introduced weeds varied in their sexual systems compared with native and introduced nonweeds. We found that introduced weeds are overrepresented by species with both male and female functions present within a single flower (hermaphrodites) whereas weeds native to the USA are overrepresented by species with male and female flowers present on a single plant (monoecious species). Overall, our results show that Baker's law is supported at the level of the sexual system, thus providing further evidence that uniparental reproduction is an important component of being either a native or introduced weed.

Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea.

Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here, we examine the potential for life-history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life-history trade-offs associated with all three traits; highly resistant populations had lower germination, shorter roots, and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.

The compounding effects of high pollen limitation, selfing rates and inbreeding depression leave a New Zealand tree with few viable offspring.

BACKGROUND AND AIMS: Interactions between species are especially sensitive to environmental changes. The interaction between plants and pollinators is of particular interest given the potential current global decline in pollinators. Reduced pollinator services can be compensated for in some plant species by self-pollination. However, if inbreeding depression is high, selfed progeny could die prior to reaching adulthood, leading to cryptic recruitment failure. METHODS: To examine this scenario, pollinator abundance, pollen limitation, selfing rates and inbreeding depression were examined in 12 populations of varying disturbance levels in Sophora microphylla (Fabaceae), an endemic New Zealand tree species. KEY RESULTS: High pollen limitation was found in all populations (average of 58 % reduction in seed production, nine populations), together with high selfing rates (61 % of offspring selfed, six populations) and high inbreeding depression (selfed offspring 86 % less fit, six populations). Pollen limitation was associated with lower visitation rates by the two endemic bird pollinators. CONCLUSIONS: The results suggest that for these populations, over half of the seeds produced are genetically doomed. This reduction in the fitness of progeny due to reduced pollinator service is probably important to population dynamics of other New Zealand species. More broadly, the results suggest that measures of seed production or seedling densities may be a gross overestimate of the effective offspring production. This could lead to cryptic recruitment failure, i.e. a decline in successful reproduction despite high progeny production. Given the global extent of pollinator declines, cryptic recruitment failure may be widespread.

Frequency-dependent pollinator discrimination acts against female plants in the gynodioecious Geranium maculatum.

BACKGROUND AND AIMS: Gynodioecy, the co-occurrence of female and hermaphroditic individuals, is thought to be an intermediate step between hermaphroditism and separate sexes, a major transition in flowering plants. Because retaining females in a population requires that they have increased seed fitness (to compensate for the lack of pollen fitness), factors that affect seed fitness are of great importance to the evolution of this mating system and have often been studied. However, factors negatively affecting female fitness are equally important and have been largely neglected. One such factor stems from female flowers being less attractive to insects than hermaphrodite flowers, thereby decreasing their relative fitness. METHODS: To test the severity and consequences of this type of pollinator discrimination in Geranium maculatum, experimental populations with the range of sex ratios observed in nature were created, ranging from 13 % to 42 % females. Pollinators were observed in order to measure the strength of discrimination, and pollen deposition and seed production of both sexes were measured to determine the fitness consequences of this discrimination. Additionally a comparison was made across the sex ratios to determine whether discrimination was frequency-dependent. KEY RESULTS: It was found that female flowers, on average, were visited at half of the rate of hermaphrodite flowers, which decreased their pollen receipt and seed production. Additionally, females were most discriminated against when rare, due to both changes in the pollinators' behaviour and a shift in pollinator composition. CONCLUSIONS: The results suggest that pollinator discrimination negatively affects females' relative fitness when they are rare. Thus, the initial spread of females in a population, the first step in the evolution of gynodioecy, may be made more difficult due to pollinator discrimination.

Sophora microphylla (Fabaceae) microsatellite markers and their utility across the genus.

PREMISE OF THE STUDY: Genus-specific microsatellite markers were developed for Sophora for population genetic and systematic studies of the group in New Zealand, and potentially elsewhere in the geographic range. • METHODS AND RESULTS: From sequencing a total genomic DNA library (using Roche 454), we identified and developed 29 polymorphic microsatellite markers for S. microphylla and S. chathamica. We tested 12 of these markers on 14 S. chathamica individuals and four S. microphylla populations. All loci amplified in both species and species-specific alleles occurred at seven loci. In S. microphylla populations, the observed and expected heterozygosities ranged from 0.000-0.960 and 0.000-0.908, respectively, with alleles per locus ranging from seven to 23. • CONCLUSIONS: The developed markers will be valuable in studies of phylogenetics, population structure, mating system, and selection of provenances for restoration projects.

Microsatellite markers for the New Zealand endemic tree Fuchsia excorticata (Onagraceae).

PREMISE OF THE STUDY: Microsatellite markers were developed from a New Zealand endemic understory tree, Fuchsia excorticata, to investigate factors affecting the mating system. • METHODS AND RESULTS: Using 454 pyrosequencing, 48 microsatellite markers were developed and tested for polymorphism within populations. Twelve of these microsatellite loci were identified as being polymorphic within at least three populations and consistently amplified in the four populations tested. These primers amplified di-, tri-, and tetranucleotide repeats with 1-10 alleles per population. • CONCLUSIONS: These results indicate the utility of microsatellite loci for future mating system and population genetic studies in F. excorticata.

Effects of environmental heterogeneity on the distribution of sexes within and among populations in a gynodioecious species, Geranium maculatum.

Populations containing both females and hermaphrodites (dimorphic) are generally found in drier sites than those with only hermaphrodites (monomorphic). The sex-differential plasticity hypothesis (SDP) suggests that this is caused by hermaphrodites reducing allocation to seeds in harsh environments, allowing female establishment. We proposed that a similar process could explain sex distribution within populations. We compared light availability and soil moisture between sites of three monomorphic and three dimorphic populations of Geranium maculatum and between microsites occupied by females and hermaphrodites within populations. We also correlated seed production in dimorphic populations with environmental measures. We found that dimorphic and monomorphic populations occurred in sites with similar soil moisture but within two dimorphic populations females occurred in drier microsites than hermaphrodites, as predicted by the SDP hypothesis. Contrary to the predictions, hermaphrodites' seed production was not influenced by the environment. Rather, females' seed production was correlated with environmental conditions in two populations, although the direction of the correlation differed between populations. Our results suggest that in this species, the SDP hypothesis does not explain sex distribution among or within populations. However, microsite environments may influence the distribution of sexes within a population and potentially aid in maintaining gynodioecy.