A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.

Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene).

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F ST ) and sequence divergence (d XY ) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.

Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene).

New species arise through the evolution of reproductive barriers between formerly interbreeding lineages. Yet, comprehensive assessments of potential reproductive barriers, which are needed to make inferences on processes driving speciation, are only available for a limited number of systems. In this study, we estimated individual and cumulative strengths of seven prezygotic and six postzygotic reproductive barriers between the recently diverged taxa Silene dioica (L.) Clairv. and S. latifolia Poiret using both published and new data. A combination of multiple partial reproductive barriers resulted in near-complete reproductive isolation between S. dioica and S. latifolia, consistent with earlier estimates of gene flow between the taxa. Extrinsic barriers associated with adaptive ecological divergence were most important, while intrinsic postzygotic barriers had moderate individual strength but contributed only little to total reproductive isolation. These findings are in line with ecological divergence as driver of speciation. We further found extensive variation in extrinsic reproductive isolation, ranging from sites with very strong selection against migrants and hybrids to intermediate sites where substantial hybridization is possible. This situation may allow for, or even promote, heterogeneous genetic divergence.

Trait differentiation and adaptation of plants along elevation gradients.

Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta-analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from 10 genomewide surveys and candidate gene approaches. We found that plants originating from high elevations were generally shorter and produced less biomass, but phenology did not vary consistently. We found significant evidence for elevation adaptation in terms of survival and biomass, but not for reproductive output. Variation in phenotypic and fitness responses to elevation across species was not related to life history traits or to environmental conditions. Molecular studies, which have focussed mainly on loci related to plant physiology and phenology, also provide evidence for adaptation along elevation gradients. Together, these studies indicate that genetically based trait differentiation and adaptation to elevation are widespread in plants. We conclude that a better understanding of the mechanisms underlying adaptation, not only to elevation but also to environmental change, will require more studies combining the ecological and molecular approaches.

Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation.

The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.

Can Evolution Supply What Ecology Demands?

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation.

Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment.

In order to investigate the role of differential adaptation for the evolution of reproductive barriers, we conducted a multi-site transplant experiment with the dioecious sister species Silene dioica and S. latifolia and their hybrids. Crosses within species as well as reciprocal first-generation (F1 ) and second-generation (F2 ) interspecific hybrids were transplanted into six sites, three within each species' habitat. Survival and flowering were recorded over 4 yr. At all transplant sites, the local species outperformed the foreign species, reciprocal F1 hybrids performed intermediately and F2 hybrids underperformed in comparison to F1 hybrids (hybrid breakdown). Females generally had slightly higher cumulative fitness than males in both within- and between-species crosses and we thus found little evidence for Haldane's rule acting on field performance. The strength of selection against F1 and F2 hybrids as well as hybrid breakdown increased with increasing strength of habitat adaptation (i.e. the relative fitness difference between the local and the foreign species) across sites. Our results suggest that differential habitat adaptation led to ecologically dependent post-zygotic reproductive barriers and drives divergence and speciation in this Silene system.

Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats.

Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early- and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.

A Single Nucleotide Deletion in Gibberellin20-oxidase1 Causes Alpine Dwarfism in Arabidopsis.

Alpine dwarfism is widely observed in alpine plant populations and often considered a high-altitude adaptation, yet its molecular basis and ecological relevance remain unclear. In this study, we used map-based cloning and field transplant experiments to investigate dwarfism in natural Arabidopsis (Arabidopsis thaliana) accessions collected from the Swiss Alps. A loss-of-function mutation due to a single nucleotide deletion in gibberellin20-oxidase1 (GA5) was identified as the cause of dwarfism in an alpine accession. The mutated allele, ga5-184, was found in two natural Arabidopsis populations collected from one geographic region at high altitude, but was different from all other reported ga5 null alleles, suggesting that this allele has evolved locally. In field transplant experiments, the dwarf accession with ga5-184 exhibited a fitness pattern consistent with adaptation to high altitude. Across a wider array of accessions from the Swiss Alps, plant height decreased with altitude of origin, but fitness patterns in the transplant experiments were variable and general altitudinal adaptation was not evident. In general, our study provides new insights into molecular basis and possible ecological roles of alpine dwarfism, and demonstrates the importance of the GA-signaling pathway for the generation of ecologically relevant variation in higher plants.

The Response of the Alpine Dwarf Shrub Salix herbacea to Altered Snowmelt Timing: Lessons from a Multi-Site Transplant Experiment.

Climate change is altering spring snowmelt patterns in alpine and arctic ecosystems, and these changes may alter plant phenology, growth and reproduction. To predict how alpine plants respond to shifts in snowmelt timing, we need to understand trait plasticity, its effects on growth and reproduction, and the degree to which plants experience a home-site advantage. We tested how the common, long-lived dwarf shrub Salix herbacea responded to changing spring snowmelt time by reciprocally transplanting turfs of S. herbacea between early-exposure ridge and late-exposure snowbed microhabitats. After the transplant, we monitored phenological, morphological and fitness traits, as well as leaf damage, during two growing seasons. Salix herbacea leafed out earlier, but had a longer development time and produced smaller leaves on ridges relative to snowbeds. Longer phenological development times and smaller leaves were associated with reduced sexual reproduction on ridges. On snowbeds, larger leaves and intermediate development times were associated with increased clonal reproduction. Clonal and sexual reproduction showed no response to altered snowmelt time. We found no home-site advantage in terms of sexual and clonal reproduction. Leaf damage probability depended on snowmelt and thus exposure period, but had no short-term effect on fitness traits. We conclude that the studied populations of S. herbacea can respond to shifts in snowmelt by plastic changes in phenology and leaf size, while maintaining levels of clonal and sexual reproduction. The lack of a home-site advantage suggests that S. herbacea may not be adapted to different microhabitats. The studied populations are thus unlikely to react to climate change by rapid adaptation, but their responses will also not be constrained by small-scale local adaptation. In the short term, snowbed plants may persist due to high stem densities. However, in the long term, reduction in leaf size and flowering, a longer phenological development time and increased exposure to damage may decrease overall performance of S. herbacea under earlier snowmelt.

Inheritance and reproductive consequences of floral anthocyanin deficiency in Silene dioica (Caryophyllaceae).

UNLABELLED: • PREMISE OF THE STUDY: Flower color is one of the most important traits for pollinator attraction. However, natural plant populations often harbor rare flower color variants resulting from mutations in biochemical pathways for floral pigment production. It is unclear how such mutations can persist because they can affect not only pollinator visitation but also plant fertility and performance.• METHODS: We collected rare white-flowered (anthocyanin-deficient) and common pink-flowered morphs of Silene dioica from natural populations in Switzerland. First- and second-generation hybrids between pink and white morphs, as well as backcrosses toward white morphs were produced, and the proportion of white-flowered offspring was determined. We compared seed siring ability and seed production between morphs using hand pollination experiments. Moreover, we scored the transfer of pollen analogues (fluorescent dyes) in a 50:50 array of the two morphs.• KEY RESULTS: The proportions of white-flowered plants in the offspring of our crosses were consistent with more than one recessive mutation as the cause of floral anthocyanin deficiency and further suggested a role of maternal effects for flower color. Seed siring ability and seed set did not differ significantly between pink and white morphs. Pollen transfer occurred preferentially within morphs.• CONCLUSIONS: Overall, our results imply that the white morph of S. dioica likely is caused by recessive mutations that do not impair reproduction. However, as this flower color polymorphism led to assortative mating in our experiment, it may represent standing genetic variation with the potential to contribute to evolutionary divergence.

Do flower color and floral scent of silene species affect host preference of Hadena bicruris, a seed-eating pollinator, under field conditions?

Specialization in plant-insect interactions is an important driver of evolutionary divergence; yet, plant traits mediating such interactions are poorly understood. In this study, we investigated how flower color and floral scent are related to seed predation by a seed-eating pollinator. We used field-transplanted recombinant F2 hybrids between Silene latifolia and S. dioica that are the preferred and alternative hosts of the moth Hadena bicruris and crosses within these species for comparison. We scored seed predation and flower color and analyzed floral scent. Pinker S. dioica-like flowers and emission of α-pinene decreased the odds of seed predation while emission of benzyl acetate and 6-methyl-5-hepten-2-one increased the odds of seed predation. Emission of these compounds did not differ significantly between the two Silene species. Our results suggest that flower color plays an important role in the specific interaction of H. bicruris with its preferred host S. latifolia. The compounds α-pinene, benzyl acetate and 6-methyl-5-hepten-2-one could represent non-specific deterrents and attractants to ovipositing moths. Alternatively, emission of these compounds could be related to herbivory or pathogen attack and act as a signal for host quality. This would weaken the predictability of the plant's costs and benefits of the interaction and act to maintain an imperfect degree of specialization.

Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent helianthus species.

While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct.

Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae).

Adaptation to different habitats is considered to be a major force in the generation of organismal diversity. Understanding the genetic mechanisms that produce such adaptations will provide insights into long-standing questions in evolutionary biology and, at the same time, improve predictions of plant responses to changing environmental conditions. Here we used semiquantitative RT-PCR to study the expression of eight candidate salt-tolerance genes in leaves of the highly salt-tolerant diploid hybrid species Helianthus paradoxus and its salt-sensitive progenitor species H. annuus and H. petiolaris. Samples were collected after germination and growth under four different treatments: nonsaline (control), near-natural saline, saline with increased K(+), and saline with decreased Mg(2+) and Ca(2+). Three individuals from three populations per species were used. The hybrid species H. paradoxus constitutively under- or overexpressed genes related to potassium and calcium transport (homologues of KT1, KT2, ECA1), suggesting that these genes may contribute to the adaptation of H. paradoxus to salinity. In two other genes, variation between populations within species exceeded species level variation. Furthermore, homologues of the potassium transporter HAK8 and of a transcriptional regulator were generally overexpressed in saline treatments, suggesting that these genes are involved in sustained growth under saline conditions in Helianthus.

Ecologically relevant genetic variation from a non-Arabidopsis perspective.

Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.

Genetic and ecological differentiation in the hybridizing campions Silene dioica and S. latifolia.

Ecological differentiation is a major contributor to the generation and maintenance of biological diversity. We investigated habitat differentiation between and within sites in the fully cross-fertile and hybridizing Silene dioica and S. latifolia using amplified fragment length polymorphisms (AFLP) profiles and corresponding vegetation relevés around individual plants. Nineteen study sites in the Swiss Alps included pure sites and contact sites (both taxa present within 30 m). In pure sites and at contact sites, the two taxa showed consistently differentiated AFLP banding patterns across regions but few discriminating bands. This indicates that although the two taxa are weakly differentiated, current introgression has not led to genome-wide admixture. Only three putative early generation hybrids were detected at contact sites. The habitats of the two taxa differed between pure sites with S. dioica occurring in moister, colder, and less-disturbed sites than S. latifolia. However, asymmetric habitat overlap was evident within contact sites found in intermediate conditions that were more similar to S. latifolia sites. This situation might favor introgression from S. dioica into S. latifolia. Evidence for habitat-genotype associations within contact sites was weak making habitat-mediated selection against intermediate phenotypes of hybrids unlikely in the contact sites investigated. We suggest that other reproductive barriers together with dispersal limitation contribute to the rarity of early generation hybrids.

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.

Response to salinity in the homoploid hybrid species Helianthus paradoxus and its progenitors H. annuus and H. petiolaris.

To contribute to the understanding of ecological differentiation in speciation, we compared salinity responses of the halophytic diploid hybrid species Helianthus paradoxus and its glycophytic progenitors Helianthus annuus and Helianthus petiolaris. Plants of three populations of each species were subjected to a control (nonsaline) and three salinity treatments, including one simulating the ion composition in the habitat of H. paradoxus. Relative to the control, saline treatments led to a 17% biomass increase in H. paradoxus while its progenitors suffered 19-33% productivity reductions and only in H. paradoxus, leaf contents of potassium, calcium, and magnesium were strongly reduced. Under all treatments, H. paradoxus allocated more resources to roots, was more succulent, and had higher leaf contents of sodium (> 200 mmol l(-1) tissue water) and sulfur than its progenitor species. These results suggest that salt tolerance and thus speciation of H. paradoxus is related to sodium replacing potassium, calcium and magnesium as vacuolar osmotica. The evolutionary and genetic mechanisms likely to be involved are discussed.

Phenotypic trade-offs in the sexual reproduction of Salicaceae from flood plains.

We studied the relationship of seed mass to seed longevity (controlled conditions) and to seed number in six species of Salicaceae (Populus nigra, Salix alba, S. daphnoides, S. elaeagnos, S. purpurea, and S. triandra) that frequently co-occur on European flood plains. These species regenerate sexually in the same habitat but differ in seed mass. Half-viability periods, i.e., the time after which 50% of the initially viable seeds no longer germinate, were short (between 6.5 ± 0.1 and 23.3 ± 0.3 d), and large numbers of seeds were produced (between 10 000 and 1 × 10(6) per plant). Mean seed mass ranged from 0.02 ± 0.001 mg in S. triandra to 0.80 ± 0.05 mg in P. nigra. Whereas seed mass was, against expectation, positively related to half-viability periods, seed number generally decreased with increasing seed mass. Thus, a phenotypic trade-off between seed mass and seed number appears to be accentuated by an increase in seed longevity with increasing seed mass.