Selection on leaf ecophysiological traits in a desert hybrid Helianthus species and early-generation hybrids

Growth and fecundity of colonizing hybrid Raphanus populations are environmentally dependent

PREMISE

Hybrid gene pools harbor more genetic variation than progenitor populations. Thus, we expect hybrid populations to exhibit more dynamic evolutionary responses to environmental variation. We ask how environmental variation experienced by adapted and transplanted populations influence the success of late-generation hybrid populations during invasion.

METHODS

For four generations, 20 wild (Raphanus raphanistrum) and 20 hybrid radish (R. sativus × R. raphanistrum) plant populations evolved under experimentally manipulated moisture conditions (dry, wet, control-sheltered, or control-unsheltered plots; i.e., evolutionary environment) in old fields near Toronto, Canada. We planted advanced-generation wild and hybrid radishes in sheltered plots and exposed them to either an evolutionary or a novel watering environment. To determine how soil moisture would influence invasion success, we compared the phenotype and fecundity of plants grown in these various environments.

RESULTS

Hybridization produced larger plants. In wet environments, hybrid seedlings emerged more frequently and expressed higher photosynthetic activity. Low-moisture, novel conditions delayed and reduced seedling emergence frequency. Hybrid plants and those that evolved under relatively wet environments exhibited higher aboveground biomass. Hybrid plants from control-sheltered plots colonizing novel moisture environments were more fecund than comparable wild plants.

CONCLUSIONS

Dry environments are less likely than other evolutionary environments to contribute colonists. However, relatively wet locations support the evolution of relatively fecund plants, especially crop-wild hybrid populations. Thus, our results provide a strong mechanistic explanation for variation in the relative success of crop-wild hybrids among study locations and a new standard for studies that assess the risk of crop-wild hybridization events.

A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency

Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; in accordance, agricultural systems have to be optimized. Several concepts and strategies should be considered to improve crop yield and quality, particularly in vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two strategies aiming to increase drought stress tolerance: (i) the use of natural genes that have evolved over time and are preserved in crop wild relatives and landraces for drought tolerance breeding using conventional and molecular methods and (ii) exploiting the reservoir of neglected and underutilized species to identify those that are known to be more drought-tolerant than conventional staple crops while possessing other desired agronomic and nutritive characteristics, as well as introducing them into existing cropping systems to make them more resilient to water deficiency conditions. In the past, the existence of drought tolerance genes in crop wild relatives and landraces was either unknown or difficult to exploit using traditional breeding techniques to secure potential long-term solutions. Today, with the advances in genomics and phenomics, there are a number of new tools available that facilitate the discovery of drought resistance genes in crop wild relatives and landraces and their relatively easy transfer into advanced breeding lines, thus accelerating breeding progress and creating resilient varieties that can withstand prolonged drought periods. Among those tools are marker-assisted selection (MAS), genomic selection (GS), and targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration of these two major strategies, the advances in conventional and molecular breeding for the drought tolerance of conventional staple crops, and the introduction of drought-tolerant neglected and underutilized species into existing production systems has the potential to enhance the resilience of agricultural production under conditions of water scarcity.

Fine root tradeoffs between nitrogen concentration and xylem vessel traits preclude unified whole-plant resource strategies in Helianthus

Recent work suggests variation in plant growth strategies is governed by a tradeoff in resource acquisition and use, ranging from a rapid resource acquisition strategy to a resource-conservative strategy. While evidence for this tradeoff has been found in leaves, knowledge of root trait strategies, and whether they reflect adaptive differentiation across environments, is limited. In the greenhouse, we investigated variation in fine root morphology (specific root length and tissue density), chemistry (nitrogen concentration and carbon:nitrogen), and anatomy (root cross-sectional traits) in populations of 26 Helianthus species and sister Phoebanthus tenuifolius. We also compared root trait variation in this study with leaf trait variation previously reported in a parallel study of these populations. Root traits varied widely and exhibited little phylogenetic signal, suggesting high evolutionary lability. Specific root length and root tissue density were weakly negatively correlated, but neither was associated with root nitrogen, providing little support for a single axis of root trait covariation. Correlations between traits measured in the greenhouse and native site characteristics were generally weak, suggesting a variety of equally viable root trait combinations exist within and across environments. However, high root nitrogen was associated with lower xylem vessel number and cross-sectional area, suggesting a tradeoff between nutrient investment and water transport capacity. This led to correlations between root and leaf traits that were not always consistent with an acquisition-conservation tradeoff at the whole-plant level. Given that roots must balance acquisition of water and nutrients with functions like anchorage, exudation, and microbial symbioses, the varied evidence for root trait covariation likely reflects the complexity of interacting selection pressures belowground. Similarly, the lack of evidence for a single acquisition-conservation tradeoff at the whole-plant level likely reflects the vastly different selection pressures shaping roots and leaves, and the resources they are optimized to obtain.

Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers

Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms by which homoploid hybrid species may arise in nature. We then present hybrid sunflowers as a case study to examine transcriptional activity of long terminal repeat retrotransposons in the annual sunflowers Helianthus annuus, Helianthus petiolaris and their homoploid hybrid derivatives (H. paradoxus, H. anomalus and H. deserticola) using high-throughput transcriptome sequencing technologies (RNAseq). Sampling homoploid hybrid sunflower taxa revealed abundant variation in TE transcript accumulation. In addition, genetic diversity for several candidate genes hypothesized to regulate TE activity was characterized. Specifically, we highlight one candidate chromatin remodelling factor gene with a direct role in repressing TE activity in a hybrid species. This paper shows that TE amplification in hybrid lineages is more idiosyncratic than previously believed and provides a first step towards identifying the mechanisms responsible for regulating and repressing TE expansions.

Direct and indirect selection on flowering time, water-use efficiency (WUE, δ (13)C), and WUE plasticity to drought in Arabidopsis thaliana

Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genetically correlated within and between different soil moisture environments? (2) Does terminal drought select for early flowering and drought escape? (3) Is WUE plasticity to drought adaptive and/or costly? We measured a suite of ecophysiological and reproductive traits on 234 spring flowering accessions of A. thaliana grown in well-watered and season-ending soil drying treatments, and quantified patterns of genetic variation, correlation, and selection within each treatment. WUE and flowering time were consistently positively genetically correlated. WUE was correlated with WUE plasticity, but the direction changed between treatments. Selection generally favored early flowering and low WUE, with drought favoring earlier flowering significantly more than well-watered conditions. Selection for lower WUE was marginally stronger under drought. There were no net fitness costs of WUE plasticity. WUE plasticity (per se) was globally neutral, but locally favored under drought. Strong genetic correlation between WUE and flowering time may facilitate the evolution of drought escape, or constrain independent evolution of these traits. Terminal drought favored drought escape in these spring flowering accessions of A. thaliana. WUE plasticity may be favored over completely fixed development in environments with periodic drought.

Needle morphological evidence of the homoploid hybrid origin of Pinus densata based on analysis of artificial hybrids and the putative parents, Pinus tabuliformis and Pinus yunnanensis

Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility

Background

Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession.

Results

While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions.

Conclusions

While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species.

Sunflower genetic, genomic and ecological resources

Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and describe the numerous publicly available resources that have enabled rapid advances in ecological and evolutionary genetics. Resources include seed collections available from germplasm centres at the USDA and INRA, genomic and EST sequences, mapping populations, genetic markers, genetic and physical maps and other forward- and reverse-genetic tools. We also discuss some of the key evolutionary, genetic and ecological questions being addressed in sunflowers, as well as gaps in our knowledge and promising areas for future research.

Reduced drought tolerance during domestication and the evolution of weediness results from tolerance-growth trade-offs

The increased reproductive potential, size, shoot allocation, and growth rate of weedy plants may result from reduced resource allocation to other aspects of plant growth and defense. To investigate whether changes in resource allocation occurred during domestication or the evolution of weediness, we compared the mycorrhizal responsiveness, growth, and drought tolerance of nine native ruderal, nine agriculturally weedy (four U.S. weedy and five Australian weedy), and 14 domesticated populations (eight ancient landraces and six improved cultivars) of the common sunflower (Helianthus annuus). Domesticated sunflower cultivars were less drought tolerant, but had higher plant growth and fecundity and coarser roots than wild populations. There were no changes in level of drought tolerance between improved cultivars and ancient landrace plants, but there was an increase in allocation to flowers with recent selection. Weedy populations were intermediate between domesticated cultivars and native ruderal populations for plant growth rate, root architecture, and drought tolerance. Weedy populations benefited most from mycorrhizal inoculation by having fewer wilted leaves and wetter soil. Overall, we found that trade-offs between drought tolerance and several aspects of plant growth, including growth rate, allocation to flowering, and root architecture, govern evolution during sunflower domestication and the invasion of disturbed habitat.

Fitness and physiology in a variable environment

The relationship between physiological traits and fitness often depends on environmental conditions. In variable environments, different species may be favored through time, which can influence both the nature of trait evolution and the ecological dynamics underlying community composition. To determine how fluctuating environmental conditions favor species with different physiological traits over time, we combined long-term data on survival and fecundity of species in a desert annual plant community with data on weather and physiological traits. For each year, we regressed the standardized annual fitness of each species on its position along a tradeoff between relative growth rate and water-use efficiency. Next, we determined how variations in the slopes and intercepts of these fitness-physiology functions related to year-to-year variations in temperature and precipitation. Years with a relatively high percentage of small rain events and a greater number of days between precipitation pulse events tended to be worse, on average, for all desert annual species. Species with high relative growth rates and low water-use efficiency had greater standardized annual fitness than other species in years with greater numbers of large rain events. Conversely, species with high water-use efficiency had greater standardized annual fitness in years with small rain events and warm temperatures late in the growing season. These results reveal how weather variables interact with physiological traits of co-occurring species to determine interannual variations in survival and fecundity, which has important implications for understanding population and community dynamics.

Hybridization and invasion: an experimental test with diffuse knapweed (Centaurea diffusa Lam.)

A number of studies have suggested a link between hybridization and invasion. In this study, we experimentally test the potential for hybridization to influence invasion through a greenhouse common garden study. Diffuse knapweed (DK) (Centaurea diffusa Lam.) was introduced to North America with admixture from spotted knapweed (SK) (Centaurea stoebe subsp. stoebe L.). Comparisons between North American DK (including hybrid phenotypes) and native (European) DK in a common garden did not reveal enhanced performance or increased phenotypic variance, suggesting that pre-introduction hybridization or, more generally, post-introduction evolutionary change has not significantly contributed to the invasion of DK. In contrast, early generation hybrids [artificially created Backcross 1 (BC1) plants] exhibited increased variance for eight of the examined traits, and greater leaf and reproductive shoot production when compared to North American DK. Individual BC1 lines differed for several traits, suggesting the importance of the cross for drawing conclusions from such comparisons. When compared to the parental species (DK and SK), the BC1 plants were not transgressive for any of the measured traits. Overall, these findings suggest that if diploid SK is introduced to North America, interspecific hybridization has the potential to result in even more aggressive invaders.

Plasticity and evolution in drought avoidance and escape in the annual plant Brassica rapa

A key question in ecological genetics is to what extent do plants adapt to changes in climatic conditions, such as drought, through plasticity or evolution. To address this question, seeds of 140 maternal families of Brassica rapa were generated from collections made before (1997) and after (2004) a natural drought. These seeds were planted in the glasshouse and grown under low-water and high-water conditions. Post-drought lines flowered earlier than pre-drought lines, showing an evolutionary shift to earlier flowering. There was significant genetic variation and genotype by environment (G × E) interactions in flowering time, indicating genetic variation in plasticity in this trait. Plants that flowered earlier had fewer leaf nodes and lower instantaneous (A/g) and integrated (δ(13)C) water use efficiency than late-flowering plants. These results suggest that B. rapa plants escape drought through early flowering rather than avoid drought through increased water use efficiency. The mechanism of this response appears to be high transpiration and inefficient water use, leading to rapid development. These findings demonstrate a trade-off between drought avoidance and escape, and indicate that, in this system, where drought acts to shorten the growing season, selection for drought escape through earlier flowering is more important than phenotypic plasticity.

Nitrogen stress response of a hybrid species: a gene expression study

BACKGROUND AND AIMS

Low soil fertility limits growth and productivity in many natural and agricultural systems, where the ability to sense and respond to nutrient limitation is important for success. Helianthus anomalus is an annual sunflower of hybrid origin that is adapted to desert sand-dune substrates with lower fertility than its parental species, H. annuus and H. petiolaris. Previous studies have shown that H. anomalus has traits generally associated with adaptation to low-fertility habitats, including a lower inherent relative growth rate and longer leaf lifetime.

METHODS

Here, a cDNA microarray is used to identify gene expression differences that potentially contribute to increased tolerance of low fertility of the hybrid species by comparing the nitrogen stress response of all three species with high- and low-nutrient treatments.

KEY RESULTS

Relative to the set of genes on the microarray, the genes showing differential expression in the hybrid species compared with its parents are enriched in stress-response genes, developmental genes, and genes involved in responses to biotic or abiotic stimuli. After a correction for multiple comparisons, five unique genes show a significantly different response to nitrogen limitation in H. anomalus compared with H. petiolaris and H. annuus. The Arabidopsis thaliana homologue of one of the five genes, catalase 1, has been shown to affect the timing of leaf senescence, and thus leaf lifespan.

CONCLUSIONS

The five genes identified in this analysis will be examined further as candidate genes for the adaptive stress response in H. anomalus. Genes that improve growth and productivity under nutrient stress could be used to improve crops for lower soil fertility which is common in marginal agricultural settings.

Contrasting drought tolerance strategies in two desert annuals of hybrid origin

Woody plants native to mesic habitats tend to be more vulnerable to drought-induced cavitation than those in xeric habitats. Cavitation resistance in herbaceous plants, however, is rarely studied and whether or not annual plants in arid habitats conform to the trends observed in woody plants is unknown. This question is addressed by comparing the hydraulic properties of annual plants endemic to relatively mesic and seasonally xeric habitats in the Great Basin Desert, in both native and experimental settings. Vulnerability to cavitation between species differed as predicted when vulnerability curves of similar-sized native individuals were compared. Contrary to expectations, Helianthus anomalus from the relatively mesic dune sites, on average, exhibited higher native embolism, lower soil-to-leaf hydraulic conductance (k(L)) and lower transpiration rates, than its xeric analogue, H. deserticola. In transplant gardens, H. anomalus' vulnerability to cavitation was unaffected by transplant location or watering treatment. In H. deserticola, however, vulnerability to cavitation varied significantly in response to watering in transplant gardens and varied as a function of stem water potential (Psi(stem)). H. deserticola largely avoided cavitation through its higher water status and generally more resistant xylem, traits consistent with a short life cycle and typical drought-escape strategy. By contrast, H. anomalus' higher native embolism is likely to be adaptive by lowering plant conductance and transpiration rate, thus preventing the loss of root-to-soil hydraulic contact in the coarse sand dune soils. For H. anomalus this dehydration avoidance strategy is consistent with its relatively long 3-4 month life cycle and low-competition habitat. We conclude that variance of hydraulic parameters in herbaceous plants is a function of soil moisture heterogeneity and is consistent with the notion that trait plasticity to fine-grained environmental variation can be adaptive.

Photosynthetic and growth responses of reciprocal hybrids to variation in water and nitrogen availability

PREMISE OF THE STUDY

Fitness of plant hybrids often depends upon the environment, but physiological mechanisms underlying the differential responses to habitat are poorly understood. We examined physiological responses of Ipomopsis species and hybrids, including reciprocal F(1)s and F(2)s, to variation in soil moisture and nitrogen. •

METHODS

To examine responses to moisture, we subjected plants to a dry-down experiment. Nitrogen was manipulated in three independent experiments, one in the field and two in common environments. •

KEY RESULTS

Plants with I. tenuituba cytoplasmic background had lower optimal soil moisture for photosynthesis, appearing better adapted to dry conditions, than plants with I. aggregata cytoplasm. This result supported a prediction from prior studies. The species and hybrids did not differ greatly in physiological responses to nitrogen. An increase in soil nitrogen increased leaf nitrogen, carbon assimilation, integrated water-use efficiency, and growth, but the increases in growth were not mediated primarily by an increase in photosynthesis. In neither the field, nor in common-garden studies, did physiological responses to soil nitrogen differ detectably across plant types, although only I. aggregata and hybrids increased seed production in the field. •

CONCLUSIONS

These results demonstrate differences in photosynthetic responses between reciprocal hybrids and suggest that water use is more important than nitrogen in explaining the relative photosynthetic performance of these hybrids compared to their parents.

Enhanced drought-tolerance in the homoploid hybrid species Pinus densata: implication for its habitat divergence from two progenitors

The homoploid hybrid species Pinus densata is restricted to alpine habitats that exceed the altitude range of its two parental species, Pinus tabulaeformis and Pinus yunnanensis. Alpine habitats usually generate cold-induced water stress in plants. To understand the ecological differentiation between these three species, we examined their physiological responses to drought stress. Potted seedlings of three species were subjected to low, mild, moderate and severe water stress in an automatic-controlled glasshouse. Fifteen indicators of fitness were measured for each species in each treatment, and most of these decreased as drought increased. Pinus densata exhibited higher fitness than both parental species in terms of total dry mass production (TDM) and long-term water use efficiency (WUE(L)) across all treatments; several other ecophysiological traits were also extreme but not across every treatment, and not always in the highest stress treatment. These results indicate that extreme characters that have become well fixed in P. densata, confer a faster seedling growth rate and more efficient water use, which in turn should confer increased drought tolerance. These traits of P. densata likely promoted its ecological separation from its parental species and facilitated its successful colonization and establishment in high-altitude habitats.

Natural variation for drought-response traits in the Mimulus guttatus species complex

Soil moisture is a key factor affecting plant abundance and distribution, both across and within species. In response to water limitation, plants have evolved numerous morphological, physiological, and phenological adaptations. In both well-watered and water-limited conditions, we identified considerable natural variation in drought-related whole-plant and leaf-level traits among closely related members of the Mimulus guttatus species complex that occupy a diversity of habitats in the field. The self-fertilizing Mimulus nasutus and serpentine-endemic Mimulus nudatus demonstrated the overall greatest tolerance to soil water limitation, exhibiting the smallest reduction in seed set relative to well-watered conditions. This may be due in part to early flowering, faster fruit development, and low stomatal density. In contrast, flowering of coastal M. guttatus was so delayed that it precluded any seed production in water-limited conditions. This range of phenotypic responses to soil water deficit in Mimulus, coupled with developing genomic resources, holds considerable promise for identifying genomic variation responsible for adaptive responses to soil water availability.

Phenotypic selection on leaf ecophysiological traits in Helianthus

Habitats that differ in soil resource availability are expected to differ for selection on resource-related plant traits. Here, we examined spatial and temporal variation in phenotypic selection on leaf ecophysiological traits for 10 Helianthus populations, including two species of hybrid origin, Helianthus anomalus and Helianthus deserticola, and artificial hybrids of their ancestral parents. Leaf traits assessed were leaf size, succulence, nitrogen (N) concentration and water-use efficiency (WUE). Biomass and leaf traits of artificial hybrids indicate that the actively moving dune habitat of H. anomalus was more growth limiting, with lower N availability but higher relative water availability than the stabilized dune habitat of H. deserticola. Habitats differed for direct selection on leaf N and WUE, but not size or succulence, for the artificial hybrids. However, within the H. anomalus habitat, direct selection on WUE also differed among populations. Across years, direct selection on leaf traits did not differ. Leaf N was the only trait for which direct selection differed between habitats but not within the H. anomalus habitat, suggesting that nutrient limitation is an important selective force driving adaptation of H. anomalus to the active dune habitat.

Physiological differences among two Penstemon species and their hybrids in field and common garden environments

Hybrids can exhibit unique combinations of the physiological traits of their parents. These particular combinations may influence hybrid fitness and the evolutionary trajectory of a hybrid zone. Here, a hybrid zone between Penstemon newberryi and Penstemon davidsonii along an elevational gradient was examined, and physiological traits of parents and hybrids were measured in their native environment and a common garden. Gas exchange rates of nine different crosses were also measured. Alpine P. davidsonii had less negative pre-dawn water potential and lower water use efficiency (WUE) than its montane relative P. newberryi in a common garden and in field measurements. The species difference in WUE was attributable to lower conductance in P. newberryi in the field, but to a higher photosynthetic rate in this species in the common garden. The alpine species took less time to produce mature fruits and reached maximum photosynthetic rate at a lower temperature. Natural hybrids were intermediate for most characters. F(1) hybrids had lower conductance than progeny of natural hybrids. The intermediate WUE of natural hybrids may be one factor that allows them to persist in intermediate environments. Comparisons of different crosses suggest that the genotypic composition of hybrids influences their physiological performance.

Selective sweeps in the homoploid hybrid species Helianthus deserticola: evolution in concert across populations and across origins

The evolution of different populations within a species in response to selective pressures can potentially happen in three different ways. It can occur in parallel, where similar changes occur independently in each population in response to selection; in concert, where the spread of an adaptive mutation across a species' range results in a single allele fixing in each population; or populations can diverge in response to local selective pressures. We explored these possibilities in populations of the homoploid hybrid species Helianthus deserticola relative to its parental species Helianthus annuus and Helianthus petiolaris using an analysis of variation in 96 expressed sequence tag-based microsatellites. A total of nine loci showed evidence consistent with recent selection at either the species or population level, although two of these genes were discarded because the apparent sweep did not occur relative to the parent from which the locus was derived. Between one and five loci showed a putative sweep across the entire species range with the same microsatellite allele fixed in each population. This pattern is consistent with evolution in concert despite geographical isolation and potential independent origins of the populations. Only one population of H. deserticola showed candidate sweeps that were unique compared to the rest of the species, and this population has also potentially experienced recent admixture with the parental species.

Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus

Natural hybridization accompanied by a shift in niche preference by hybrid genotypes can lead to hybrid speciation. Natural selection may cause the fixation of advantageous alleles in the ecologically diverged hybrids, and the loci experiencing selection should exhibit a reduction in allelic diversity relative to neutral loci. Here, we analyzed patterns of genetic diversity at 59 microsatellite loci associated with expressed sequence tags (ESTs) in a homoploid hybrid sunflower species, Helianthus anomalus. We used two indices, ln RV and ln RH, to compare variation and heterozygosity (respectively) at each locus between the hybrid species and its two parental species, H. annuus and H. petiolaris. Mean values of ln RV and ln RH were significantly lower than zero, which implies that H. anomalus experienced a population bottleneck during its recent evolutionary history. After correcting for the apparent bottleneck, we found six loci with a significant reduction in variation or with heterozygosity in the hybrid species, compared to one or both of the parental species. These loci should be viewed as a ranked list of candidate loci, pending further sequencing and functional analyses. Sequence data were generated for two of the candidate loci, but population genetics tests failed to detect deviations from neutral evolution at either locus. Nonetheless, a greater than eight-fold excess of nonsynonymous substitutions was found near a putative N-myristoylation motif at the second locus (HT998), and likelihood-based models indicated that the protein has been under selection in H. anomalus in the past and, perhaps, in one or both parental species. Finally, our data suggest that selective sweeps may have united populations of H. anomalus isolated by a mountain range, indicating that even low gene-flow species may be held together by the spread of advantageous alleles.

Plastic responses to temporal variation in moisture availability: consequences for water use efficiency and plant performance

The ability to appropriately modify physiological and morphological traits in response to temporal variation should increase fitness. We used recombinant hybrid plants generated by crossing taxa in the Piriqueta caroliniana complex to assess the effects of individual leaf traits and trait plasticities on growth in a temporally variable environment. Recombinant hybrids were used to provide a wide range of trait expression and to allow an assessment of the independent effects of individual traits across a range of genetic backgrounds. Hybrid genotypes were replicated through vegetative propagation and planted in common gardens at Archbold Biological Station in Venus, Florida, where they were monitored for growth, leaf morphological characters, and integrated water use efficiency (WUE) (C isotope ratio; delta(13)C) for two successive seasons. Under wet conditions only leaf area had significant effects on plant growth, but as conditions became drier, growth rates were greatest in plants with narrow leaves and higher trichome densities. Plants with higher WUE exhibited increased growth during the dry season but not during the wet season. WUE during the dry season was increased for plants with smaller, narrower leaves that had higher trichome densities and increased reflectance. Examination of alternative path models revealed that during the dry season leaf traits had significant effects on plant growth only through their direct effects on WUE, as estimated from delta(13)C. Over the entire growing season, plants with a greater ability to produce smaller and narrower leaves with higher trichome densities in response to reduced water availability had the greatest growth rate. These findings suggest that plants making appropriate changes to leaf morphology as conditions became dry had increased WUE, and that the ability to adjust leaf phenotypes in response to environmental variation is a mechanism by which plants increase fitness.

The speed of ecological speciation

Adaptation can occur on ecological time-scales (contemporary evolution) and adaptive divergence can cause reproductive isolation (ecological speciation). From the intersection of these two premises follows the prediction that reproductive isolation can evolve on ecological time-scales. We explore this possibility in theory and in nature. Finding few relevant studies, we examine each in some detail. THEORY: Several models have demonstrated that ecological differences can drive the evolution of partial reproductive barriers in dozens to hundreds of generations. Barriers likely to evolve quickly include dispersal rate, habitat preference and selection against migrants/hybrids. PLANTS: Adjacent populations adapting to different fertilizer treatments or to mine tailings can develop reproductive barriers within at least 100 generations. These barriers include differences in flowering time and selection against migrants/hybrids. INVERTEBRATES: Populations on native and introduced host plants can manifest reproductive barriers in dozens to hundreds of generations. These barriers include local host preference and selection against migrants/hybrids. VERTEBRATES: Salmon adapting to divergent breeding environments can show restricted gene flow within at least 14 generations. Birds evolving different migratory routes can mate assortatively within at least 10-20 generations. Hybrid sculpins can become isolated from their ancestral species within at least 20-200 generations. Ecological speciation can commence within dozens of generations. How far it goes is an important question for future research.

Reconstructing the history of selection during homoploid hybrid speciation

This study aims to identify selection pressures during the historical process of homoploid hybrid speciation in three Helianthus (sunflower) hybrid species. If selection against intrinsic genetic incompatibilities (fertility selection) or for important morphological/ecological traits (phenotypic selection) were important in hybrid speciation, we would expect this selection to have influenced the parentage of molecular markers or chromosomal segments in the hybrid species' genomes. To infer past selection, we compared the parentage of molecular markers in high-density maps of the three hybrid species with predicted marker parentage from an analysis of fertility selection in artificial hybrids and from the directions of quantitative trait loci effects with respect to the phenotypes of the hybrid species. Multiple logistic regression models were consistent with both fertility and phenotypic selection in all three species. To further investigate traits under selection, we used a permutation test to determine whether marker parentage predicted from groups of functionally related traits differed from neutral expectations. Our results suggest that trait groups associated with ecological divergence were under selection during hybrid speciation. This study presents a new method to test for selection and supports earlier claims that fertility selection and phenotypic selection on ecologically relevant traits have operated simultaneously during sunflower hybrid speciation.

Microsatellite signature of ecological selection for salt tolerance in a wild sunflower hybrid species, Helianthus paradoxus

The hybrid sunflower species Helianthus paradoxus inhabits sporadic salt marshes in New Mexico and southwest Texas, USA, whereas its parental species, Helianthus annuus and Helianthus petiolaris, are salt sensitive. Previous studies identified three genomic regions - survivorship quantitative trait loci (QTLs) - that were under strong selection in experimental hybrids transplanted into the natural habitat of H. paradoxus. Here we ask whether these same genomic regions experienced significant selection during the origin and evolution of the natural hybrid, H. paradoxus. This was accomplished by comparing the variability of microsatellites linked to the three survivorship QTLs with those from genomic regions that were neutral in the experimental hybrids. As predicted if one or more selective sweeps had occurred in these regions, microsatellites linked to the survivorship QTLs exhibited a significant reduction in diversity in populations of the natural hybrid species. In contrast, no difference in diversity levels was observed between the two microsatellite classes in parental populations.

Genetic architecture of leaf ecophysiological traits in Helianthus

We investigated quantitative trait loci (QTLs) for several leaf chemistry traits in early-generation hybrids between Helianthus annuus and Helianthus petiolaris, the parental species of the ancient diploid hybrid sunflower species Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus. We grew individuals of a second-generation backcross (BC(2)) toward H. petiolaris under optimum conditions in a glass house experiment. Trait values were measured once for each individual. In addition, genotypic data previously determined for each individual were employed for composite interval mapping of QTLs. We detected QTLs for leaf carbon concentration, leaf nitrogen concentration, leaf nitrogen per unit area, and photosynthetic nitrogen use efficiency. Leaf carbon isotope discrimination (delta(13)C) and leaf nitrogen isotopic composition (delta(15)N) were analyzed, but no significant QTLs were found for these traits. Interestingly, two neighboring loci explained a relatively large percentage of the variation in leaf nitrogen per unit area. This was notable because leaf nitrogen has been shown to strongly affect the fitness of early-generation sunflower hybrids in the H. anomalus habitat, and QTLs of large effect are expected to respond relatively quickly to selection. We speculate that the genetic architecture underlying leaf nitrogen may have facilitated the colonization of active desert sand dunes by H. anomalus.

Phenotypic selection on leaf water use efficiency and related ecophysiological traits for natural populations of desert sunflowers

Plant water-use efficiency (WUE) is expected to affect plant fitness and thus be under natural selection in arid habitats. Although many natural population studies have assessed plant WUE, only a few related WUE to fitness. The further determination of whether selection on WUE is direct or indirect through functionally related traits has yielded no consistent results. For natural populations of two desert annual sunflowers, Helianthus anomalus and H. deserticola, we used phenotypic selection analysis with vegetative biomass as the proxy for fitness to test (1) whether there was direct and indirect selection on WUE (carbon isotope ratio) and related traits (leaf N, area, succulence) and (2) whether direct selection was consistent with hypothesized drought/dehydration escape and avoidance strategies. There was direct selection for lower WUE in mesic and dry H. anomalus populations, consistent with dehydration escape, even though it is the longer lived of the two species. For mesic H. anomalus, direct selection favored lower WUE and higher N, suggesting that plants may be "wasting water" to increase N delivery via the transpiration stream. For the shorter lived H. deserticola in the direr habitat, there was indirect selection for lower WUE, inconsistent with drought escape. There was also direct selection for higher leaf N, succulence and leaf size. There was no direct selection for higher WUE consistent with dehydration avoidance in either species. Thus, in these natural populations of two desert dune species higher fitness was associated with some combination direct and indirect selection for lower WUE, higher leaf N and larger leaf size. Our understanding of the adaptive value of plant ecophysiological traits will benefit from further consideration of related traits such as leaf nitrogen and more tests in natural populations.

Hybridization and the colonization of novel habitats by annual sunflowers

Although invasive plant species often have a hybrid ancestry, unambiguous evidence that hybridization has stimulated the evolution of invasive behaviors has been difficult to come by. Here, we briefly review how hybridization might contribute to the colonization of novel habitats, range expansions, and invasiveness and then describe work on hybrid sunflowers that forges a direct link between hybridization and ecological divergence. We first discuss the invasion of Texas by the common sunflower and show that the introgression of chromosomal segments from a locally adapted species may have facilitated range expansion. We then present evidence that the colonization of sand dune, desert floor, and salt marsh habitats by three hybrid sunflower species was made possible by selection on extreme or "transgressive" phenotypes generated by hybridization. This body of work corroborates earlier claims regarding the role of hybridization in adaptive evolution and provides an experimental and conceptual framework for ongoing studies in this area.

Microarray analysis reveals differential gene expression in hybrid sunflower species

This paper describes the creation of a cDNA microarray for annual sunflowers and its use to elucidate patterns of gene expression in Helianthus annuus, Helianthus petiolaris, and the homoploid hybrid species Helianthus deserticola. The array comprises 3743 ESTs (expressed sequence tags) representing approximately 2897 unique genes. It has an average clone/EST identity rate of 91%, is applicable across species boundaries within the annual sunflowers, and shows patterns of gene expression that are highly reproducible according to real-time RT-PCR (reverse transcription-polymerase chain reaction) results. Overall, 12.8% of genes on the array showed statistically significant differential expression across the three species. Helianthus deserticola displayed transgressive, or extreme, expression for 58 genes, with roughly equal numbers exhibiting up- or down-regulation relative to both parental species. Transport-related proteins were strongly over-represented among the transgressively expressed genes, which makes functional sense given the extreme desert floor habitat of H. deserticola. The potential adaptive value of differential gene expression was evaluated for five genes in two populations of early generation (BC2) hybrids between the parental species grown in the H. deserticola habitat. One gene (a G protein-coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat.

Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species

New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies.

Adaptive introgression of herbivore resistance traits in the weedy sunflower Helianthus annuus

The role of hybridization in adaptive evolution is contentious. While many cases of adaptive trait introgression have been proposed, the relevant traits have rarely been identified, resulting in a lack of clear examples of this process. Here, we examine a purported case of adaptive introgression in which the annual sunflower Helianthus annuus annuus has captured alleles from a congener (Helianthus debilis) to form a stabilized hybrid, Helianthus annuus texanus. We tested the hypotheses that herbivore resistance traits have introgressed from H. debilis to H. annuus and have increased adaptation in the latter. In two common gardens, fitness (estimated by seed production) was on average 55% higher in H. a. texanus than in H. a. annuus. For H. a. texanus, three damage traits (of seven tested) differed significantly from the H. a. annuus parent in one or both sites and were shifted in the direction of the more resistant H. debilis. Natural selection favored H. a. annuusxH. debilis BC(1) hybrids (synthesized to mimic the ancestors of H. a. texanus) with H. debilis-like resistance to seed midges Neolasioptera helianthis and to receptacle/seed feeding Lepidoptera at one or both sites. Assuming similar herbivore pressures in the past, these results suggest that introgression of biotic resistance traits was important in the adaptation of H. annuus to central and southern Texas.

Environmental stressors differentially affect leaf ecophysiological responses in two Ipomopsis species and their hybrids

The recombination that follows natural hybridization may produce hybrid genotypes with traits that are intermediate or extreme relative to the parental species, and these traits may influence the relative fitness of the hybrids. Here we examined leaf ecophysiological traits that may influence fitness patterns in a natural plant hybrid zone. We compared the biochemical photosynthetic capacity of Ipomopsis aggregata, I. tenuituba, and early generation hybrids, as well as their photosynthetic responses to varying light and temperature, two abiotic factors found to differ among sites along the hybrid zone. In general, ecophysiological traits expressed in these plants were consistent with their natural habitat, even when grown under common greenhouse conditions. I. tenuituba reached higher photosynthetic rates (A) at higher light levels than I. aggregata, and also had a higher optimal temperature for photosynthesis (Topt). This suite of traits may reflect adaptations to the more exposed, rocky sites where I. tenuituba is found, compared to the more vegetated, mesic I. aggregata site. Hybrids had characters that were largely intermediate or tenuituba-like, but particular individual hybrids were extreme for some traits, including light saturation level, light-saturated A, and Topt. Many of these traits are consistent with adaptations reported for plants found in warm, dry sites, so they may put certain hybrids at an advantage at the relatively xeric center of the natural hybrid zone.

Nutrient and water addition effects on day- and night-time conductance and transpiration in a C3 desert annual

Recent research has shown that many C3 plant species have significant stomatal opening and transpire water at night even in desert habitats. Day-time stomatal regulation is expected to maximize carbon gain and prevent runaway cavitation, but little is known about the effect of soil resource availability on night-time stomatal conductance (g) and transpiration (E). Water (low and high) and nutrients (low and high) were applied factorially during the growing season to naturally occurring seedlings of the annual Helianthus anomalus. Plant height and biomass were greatest in the treatment where both water and nutrients were added, confirming resource limitations in this habitat. Plants from all treatments showed significant night-time g (approximately 0.07 mol m(-2) s(-1)) and E (approximately 1.5 mol m(-2) s(-1)). In July, water and nutrient additions had few effects on day- or night-time gas exchange. In August, however, plants in the nutrient addition treatments had lower day-time photosynthesis, g and E, paralleled by lower night-time g and E. Lower predawn water potentials and higher integrated photosynthetic water-use efficiency suggests that the nutrient addition indirectly induced a mild water stress. Thus, soil resources can affect night-time g and E in a manner parallel to day-time, although additional factors may also be involved.

Re-creating ancient hybrid species' complex phenotypes from early-generation synthetic hybrids: three examples using wild sunflowers

Can the complex phenotypes that characterize naturally occurring hybrid species be re-created in early-generation artificial hybrids? We address this question with three homoploid hybrid species (Helianthus anomalus, Helianthus deserticola, Helianthus paradoxus) and their ancestral parents (Helianthus annuus, Helianthus petiolaris) that are phenotypically distinct and ecologically differentiated. These species, and two synthetic hybrid populations of the ancestral parents, were characterized for morphological, physiological, and life-history traits in greenhouse studies. Among the synthetic hybrids, discriminant analysis identified a few individuals with the multitrait phenotype of the natural hybrid species: 0.7%-1.1% were H. anomalus-like, 0.5%-13% were H. deserticola-like, and only 0.4% were H. paradoxus-like. These relative frequencies mirror previous findings that genetic correlations are favorable for generating the hybrid species' phenotypes, and they correspond well with phylogeographic evidence that demonstrates multiple natural origins of H. deserticola and H. anomalus but a single origin for H. paradoxus. Even though synthetic hybrids with hybrid species phenotypes are rare, their phenotypic correlation matrices share most of the same principal components (eigenvectors), setting the stage for predictable recovery of hybrid species' phenotypes from different hybrid populations. Our results demonstrate past hybridization could have generated hybrid species-like multitrait phenotypes suitable for persistence in their respective environments in just three generations after initial hybridization.

The ecological genetics of homoploid hybrid speciation

Our understanding of homoploid hybrid speciation has advanced substantially since this mechanism of species formation was codified 50 years ago. Early theory and research focused almost exclusively on the importance of chromosomal rearrangements, but it later became evident that natural selection, specifically ecological selection, might play a major role as well. In light of this recent shift, we present an evaluation of ecology's role in homoploid hybrid speciation, with an emphasis on the genetics underlying ecological components of the speciation process. We briefly review new theoretical developments related to the ecology of homoploid hybrid speciation; propose a set of explicit, testable questions that must be answered to verify the role of ecological selection in homoploid hybrid speciation; discuss published work with reference to these questions; and also report new data supporting the importance of ecological selection in the origin of the homoploid hybrid sunflower species Helianthus deserticola. Overall, theory and empirical evidence gathered to date suggest that ecological selection is a major factor promoting homoploid hybrid speciation, with the strongest evidence coming from genetic studies.