Genetic structure of hybrid zones between Silene latifolia and Silene dioica (Caryophyllaceae): evidence for introgressive hybridization

Asymmetric Introgression and Cryptic Natural Hybridization between Two Species of Teucrium Section Polium (Lamiaceae) on the Balkan Peninsula

In this work, we analyzed the morphology and genetic structure of Teucrium montanum, T. capitatum and their hybrid T. × rohlenae from three syntopic populations. A morphometric study showed that the parents and their hybrids exhibited continuous morphological variation, with the hybrid positioned exactly between the parents. Genetic analysis revealed that plants morphologically identified as T. × rohlenae are fertile hybrids that produce hybrid swarms dominated by later-generation hybrids. This suggests that introgression, rather than speciation, is the more likely outcome of hybridization between these plant species. The extent and direction of gene flow between the two species differed markedly between the three syntopic localities. At the Trilj locality, it was clearly unidirectional, with T. capitatum playing the dominant role. At the Sićevo locality, gene flow was slightly asymmetric, favoring the genetic background of T. capitatum, while at the Sliven site, it was completely asymmetric in the opposite direction. The extreme case of unidirectional gene flow was observed at the Trilj locality where plants morphologically identified as T. montanum could not be genetically distinguished from T. capitatum. This suggests that interspecific hybridization occurred long ago, leading to introgression and cryptic hybrids, blurring of species boundaries and generating evolutionary noise.

Seed shape and size of Silene latifolia, differences between sexes, and influence of the parental genome in hybrids with Silene dioica

Introduction

Plants undergo various natural changes that dramatically modify their genomes. One is polyploidization and the second is hybridization. Both are regarded as key factors in plant evolution and result in phenotypic differences in different plant organs. In Silene, we can find both examples in nature, and this genus has a seed shape diversity that has long been recognized as a valuable source of information for infrageneric classification.

Methods

Morphometric analysis is a statistical study of shape and size and their covariations with other variables. Traditionally, seed shape description was limited to an approximate comparison with geometric figures (rounded, globular, reniform, or heart-shaped). Seed shape quantification has been based on direct measurements, such as area, perimeter, length, and width, narrowing statistical analysis. We used seed images and processed them to obtain silhouettes. We performed geometric morphometric analyses, such as similarity to geometric models and elliptic Fourier analysis, to study the hybrid offspring of S. latifolia and S. dioica.

Results

We generated synthetic tetraploids of Silene latifolia and performed controlled crosses between diploid S. latifolia and Silene dioica to analyze seed morphology. After imaging capture and post-processing, statistical analysis revealed differences in seed size, but not in shape, between S. latifolia diploids and tetraploids, as well as some differences in shape among the parentals and hybrids. A detailed inspection using fluorescence microscopy allowed for the identification of shape differences in the cells of the seed coat. In the case of hybrids, differences were found in circularity and solidity. Overal seed shape is maternally regulated for both species, whereas cell shape cannot be associated with any of the sexes.

Discussion

Our results provide additional tools useful for the combination of morphology with genetics, ecology or taxonomy. Seed shape is a robust indicator that can be used as a complementary tool for the genetic and phylogenetic analyses of Silene hybrid populations.

Molecular and morphological evidence of hybridization between two dimorphic sympatric species of Fuchsia (Onagraceae)

Hybridization is commonly reported in angiosperms, generally based on morphology, and in few cases confirmed by molecular markers. Fuchsia has a long tradition of ornamental cultivars with different hybrids produced by artificial crosses, so natural hybridization between sympatric Fuchsia species could be common. Natural hybridization between F. microphylla and F. thymifolia was tested using six newly developed microsatellites for F. microphylla in addition to other molecular markers with codominant and maternal inheritance. Geometric morphometrics of leaves and floral structures were also used to identify putative hybrids. Hybrids showed a different degree of genetic admixture between both parental species. Chloroplast DNA (cpDNA) sequences indicated that hybridization occurs in both directions, in fact, some of the hybrids showed new haplotypes for cpDNA and ITS (internal transcriber spacer of nuclear ribosomal RNA genes) sequences. The morphology of hybrid individuals varied between the two parental species, but they could be better identified by their leaves and floral tubes. Our study is the first to confirm the hybridization in natural populations of Fuchsia species and suggests that hybridization has probably occurred repeatedly throughout the entire distribution of the species. Phylogeographic analysis of both species will be essential to understanding the impact of hybridization throughout their complete distribution.

Pericentromeric recombination suppression and the 'large X effect' in plants

X chromosome was reported to be a major contributor to isolation between closely related species-the 'large X' effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plant Silene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE in S. latifolia is caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression in S. latifolia and its close cross-compatible relative S. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE in S. latifolia and S. dioica.

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.

Effects of the neo-X chromosome on genomic signatures of hybridization in Rumex hastatulus

Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species with evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. Cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X chromosome, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly steeper clines than the genome average were located on the neo-X. Our data are consistent with a role for neo-sex chromosomes in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones for understanding the evolution of sex chromosomes.

Hybridization and introgression of native and foreign Sorbus tree species in unique environments of protected mountainous areas

Hybridization and introgression are important processes influencing the genetic diversity and evolution of species. These processes are of particular importance in protected areas, where they can lead to the formation of hybrids between native and foreign species and may ultimately result in the loss of parental species from their natural range. Despite their importance, the contribution of hybridization and introgression to genetic diversity in Sorbus genus remains not fully recognized. We analysed the genetic and morphological variability of several Sorbus species including native (Sorbus aria), foreign (S. intermedia) and potentially hybrid (S. carpatica) individuals from the Polish Carpathian range. Patterns of variation at 13 nuclear microsatellite loci show hybridization between the tested species and confirm the existence of the hybrid form S. carpatica. Biometric analysis on leaves, based of 10 metric features and three parameters, identified several characters for preliminary taxonomic classification; however, none of them could be used as a fully diagnostic marker for faultless annotation of S. intermedia and S. carpatica. The genetic structure analysis indicated complex patterns of population differentiation and its diverse origin. The results allow assessment of genetic variation and identification of parental species participating in hybridization. This knowledge will advance the management of genetic diversity and development of conservation strategies for efficient maintenance of the unique protected ecosystem.

Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain

Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.

Genetic diversity and structure of the hedgehogs Erinaceus europaeus and Erinaceus roumanicus: evidence for ongoing hybridization in Eastern Europe

Secondary contact zones between related species are key to understanding speciation mechanisms. The Central European sympatry zone of West European (Erinaceus europaeus) and northern white-breasted (Erinaceus roumanicus) hedgehogs is well studied, whereas data on the Eastern European sympatry zone are scarce. We examined the genetic variation in Russian populations using the mitochondrial Cytb gene, TTR intron 1 and 11 microsatellites to assess genetic variability and distribution patterns. In contrast to the Central European sympatry zone, we found evidence of ongoing hybridization between the two species in the sympatry zone of European Russia, where the proportion of individuals with mixed ancestry was c. 20%. Our data indicate bi-directional mtDNA introgression, but with a higher frequency of E. europaeus haplotypes in hybrids. The proportion of pure specimens with introgressed mitotypes is higher in E. roumanicus than in E. europaeus. Nuclear data showed the prevalence of the genetic contribution from E. roumanicus in admixed individuals. Demographic analyses indicated recent population growth in E. europaeus and little change in E. roumanicus, suggesting that E. europaeus colonized East Europe later than E. roumanicus.

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.

Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization and Divergence With the Balearic Island Populations

Reconstructing the phylogenetic relationships within Caryophyllaceae tribe Sileneae has been obscured by hybridization and incomplete lineage sorting. Silene is the largest genus in the Caryophyllaceae, and unraveling its evolutionary history has been particularly challenging. In order to infer the phylogenetic relationships among the five species in Silene section Psammophilae, we have performed a genome skimming approach to acquire the complete plastid genome (cpDNA), nuclear ribosomal cistron (nrDNA), and partial mitochondrial genome (mtDNA). We have included 26 populations, representing the range of each species' distribution. This section includes five morphologically similar species endemic to the Iberian Peninsula and Balearic Islands (Ibiza and Formentera), yet some of them occupy distinct edaphic habitats (e.g. maritime sands, calcareous sandstones). In addition to phylogeographic analyses, genetic structuring using the chloroplast data set was inferred with Discriminant Analysis of Principal Components (DAPC), analyses of molecular variance (AMOVA), and a partial Mantel test. Reference-guided assembly of 50 bp single-end and 250 bp paired-end Illumina reads produced the nearly complete cpDNA genome (154 kbp), partial mtDNA genome (from 81 to 114 kbp), and the nrDNA cistron (6.4 kbp). Selected variable regions of the cpDNA and mtDNA assemblies were confirmed by Sanger sequencing. Phylogenetic analyses of the mainland populations reveal incongruence among the three genomes. None of the three data sets produced relationships consistent with taxonomy or geography. In contrast, Silene cambessedesii, present in the Balearic Islands, is the only species that forms a strongly supported monophyletic clade in the cpDNA genome and is strongly differentiated with respect to the remaining taxa of the Iberian Peninsula. These results contrast with those obtained for mainland populations. Across the entire analysis, only one well-supported mainland clade of Silene littorea and Silene stockenii emerges from the southern region of the Iberian Peninsula. DAPC and AMOVA results suggest the absence of genetic structure among mainland populations of Silene section Psammophilae, whereas partial Mantel test discarded spatial correlation of genetic differentiation. The widespread incongruence between morphology-based taxonomic boundaries and phylogeography suggests a history of interspecific hybridization, in which only a substantial geographic barrier, like isolation by the Mediterranean Sea, was sufficient to create and maintain species boundaries in Silene section Psammophilae.

Importance of Pollinator-Mediated Interspecific Pollen Transfer for Angiosperm Evolution

Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.

Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species

The evolution of sexual dimorphism in species with separate sexes is influenced by the resolution of sexual conflicts creating sex differences through genetic linkage or sex-biased expression. Plants with different degrees of sexual dimorphism are thus ideal to study the genetic basis of sexual dimorphism. In this study we explore the genetic architecture of sexual dimorphism between Silene latifolia and Silene dioica. These species have chromosomal sex determination and differ in the extent of sexual dimorphism. To test whether QTL for sexually dimorphic traits have accumulated on the sex chromosomes and to quantify their contribution to species differences, we create a linkage map and performed QTL analysis of life history, flower and vegetative traits using an unidirectional interspecific F2 hybrid cross. We found support for an accumulation of QTL on the sex chromosomes and that sex differences explained a large proportion of the variance between species, suggesting that both natural and sexual selection contributed to species divergence. Sexually dimorphic traits that also differed between species displayed transgressive segregation. We observed a reversal in sexual dimorphism in the F2 population, where males tended to be larger than females, indicating that sexual dimorphism is constrained within populations but not in recombinant hybrids. This study contributes to the understanding of the genetic basis of sexual dimorphism and its evolution in Silene.

Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length

Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations.

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.

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.

Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet

Ecological speciation is an important factor in the diversification of plants. The distribution of the woody species Rhododendron indicum, which grows along rivers and is able to withstand water flow when rivers flood (i.e. it is a rheophyte), is disjunct, in contrast to the widespread distribution of its relative, Rhododendron kaempferi. This study aimed to elucidate the phylogenetic relationships between R. indicum and R. kaempferi and the evolutionary processes that gave rise to them. The sequences of three non-coding chloroplast DNA regions (total length 1977 bp) were obtained from 21 populations covering the ranges of the two species. In addition, genome-wide SNPs were genotyped from 20 populations using a genotyping by sequencing method. Leaf morphologies were measured for eight representative populations. Two chloroplast DNA haplotypes, which were detected in R. indicum, were shared between the two species. Genome-wide SNPs identified two lineages in R. indicum and these lineages did not constitute a monophyletic group. Each of these two lineages was related to geographically close populations of R. kaempferi. Leaf morphology, which is a characteristic feature in rheophytes, was not differentiated between the two lineages in R. indicum. The morphological similarity between the two heterogeneous lineages may be a result of parallel evolution from R. kaempferi or of introgressive hybridization between the species due to strong selective pressure imposed by flooding.

Asymmetrical natural hybridization varies among hybrid swarms between two diploid Rhododendron species

Background and Aims

The extent to which hybridization leads to gene flow between plant species depends on the structure of hybrid populations. However, if this varies between locations, species barriers might prove permeable in some locations but not in others. To assess possible variation in hybrid population structure, the magnitude and direction of natural hybridization between two Chinese endemic species, Rhododendron spiciferum and Rhododendron spinuliferum , were evaluated.

Methods

Thirteen nuclear microsatellite markers were employed to characterize 566 individuals collected from 15 non-allopatric populations and nine allopatric parental populations. Chloroplast DNA (cpDNA) sequences were obtained from a subset of samples. Genetic structure and direction of gene flow was determined using a combination of STRUCTURE and NEWHYBRIDS analysis.

Key Results

Nuclear analysis revealed that parental taxa formed two genetically distinct clusters and hybrids shared the genetic background of both parents and did not form a separate genetic lineage. Overall, hybrid swarms were dominated by early- and later-generation hybrids, with a significantly higher proportion of hybrids (59·6 %) possessing >50 % R. spiciferum-like nuclear germplasm. The cpDNA analysis further indicated that a significantly greater proportion of hybrids (61·1 %) possessed the R. spiciferum cpDNA haplotype.

Conclusions

Gene flow between R. spiciferum and R. spinuliferum was found to be bidirectional in 14 of the 15 hybrid swarms and asymmetrical in six hybrid swarms. Asymmetrical gene flow was evident for only nuclear DNA (nDNA) in two populations, for only cpDNA in three populations, and for both nDNA and cpDNA in one population. Collectively, the variation in genetic structure found among the 15 hybrid swarms suggests that introgression rather than hybrid speciation is a more likely outcome of hybridization between these hybridizing taxa.

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.

Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow

DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.

Environmental (in)dependence of a hybrid zone: Insights from molecular markers and ecological niche modeling in a hybrid zone of Origanum (Lamiaceae) on the island of Crete

The role of environment and the relative significance of endogenous versus exogenous selection in shaping hybrid zones have been crucial issues in the studies of hybridization. Recent advances in ecological niche modeling (ENM) offer new methodological tools, especially in combination with the genotyping of individuals in the hybrid zone. Here, we study the hybrid zone between the widely known spices Origanum onites and Origanum vulgare ssp. hirtum in Crete. We analyze the genetic structure of both parental taxa and their hybrid Origanum × intercendens using AFLP markers on 15 sympatric and 12 allopatric populations and employ ecological niche modeling and niche similarity tests to study their niche patterns. We complement these analyses with seed viability measurements. Our study revealed that the hybridizing taxa O. onites and O. vulgare ssp. hirtum and the resulting genotypic classes showed geographical and environmental niche similarities based on the predictions of ENMs and the subsequent similarity tests. The occurrence of the hybrid zone is not directly dependent on environmental factors which favor the fitness of the hybrid compared to the parental taxa, but rather on aspects such as historical factors and management practices, which may contribute to the localization and maintenance of the contact zone between parental species. Our results suggest that if a minimum required niche differentiation between genotypic classes is not achieved, environmental dependence might not have a prominent role on the outcome of the hybridization.

Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs

The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining region and several genes that are partially sex-linked in Silene latifolia, using Silene dioica, a closely related dioecious plants whose XY sex chromosome system is inherited from a common ancestor. The S. latifolia pseudoautosomal region (PAR) includes several genes extremely closely linked to the fully Y-linked region. These genes were added to an ancestral PAR of the sex chromosome pair in two distinct events probably involving translocations of autosomal genome regions causing multiple genes to become partially sex-linked. Close linkage with the PAR boundary must have evolved since these additions, because some genes added in both events now show almost complete sex linkage in S. latifolia. We compared diversity patterns of five such S. latifolia PAR boundary genes with their orthologues in S. dioica, including all three regions of the PAR (one gene that was in the ancestral PAR and two from each of the added regions). The results suggest recent recombination suppression in S. latifolia, since its split from S. dioica.

The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome

The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7)  years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later-generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.

Evidence for asymmetrical hybridization despite pre- and post-pollination reproductive barriers between two Silene species

Interspecific hybridization is widespread among plants; nevertheless, pre- and post-zygotic isolating mechanisms may maintain species integrity for interfertile species in sympatry despite some gene flow. Interspecific hybridization and potential isolating barriers were evaluated between co-flowering Silene asclepiadea and Silene yunnanensis in an alpine community in southwest China. We investigated morphological and molecular (nuclear microsatellites and chloroplast gene sequence) variation in sympatric populations of S. asclepiadea and S. yunnanensis. Additionally, we analyzed pollinator behaviour and compared reproductive success between the putative hybrids and their parental species. Both the molecular and morphological data indicate that there were putative natural hybrids in the field, with S. asclepiadae the ovule parent and S. yunnanensis the pollen parent. Bumblebees were the primary visitors to S. asclepiadae and putative hybrids, while butterflies were the primary visitors to S. yunnanensis Pollen production and viability were significantly lower in putative hybrids than the parental species. The direction of hybridization is quite asymmetric from S. yunnanensis to S. asclepiadea Protandry combined with later peak flowering of S. yunnanensis, and pollinator preference may have contributed to the asymmetric pattern of hybridization, but putative hybrids were rare. Our results thus suggest that despite gene flow, S. asclepiadea and S. yunnanensis can maintain species boundaries, perhaps as a result of floral isolation and low fecundity of the hybrids.

Evidence for a bimodal distribution of hybrid indices in a hybrid zone with high admixture

The genetic structure of a hybrid zone can provide insights into the relative roles of the various factors that maintain the zone. Here, we use a multilocus approach to characterize a hybrid zone between two subspecies of killifish (Fundulus heteroclitus, Walbaum 1792) found along the Atlantic coast of North America. We first analysed clinal variation along the Atlantic coast using a single-nucleotide polymorphism in the mitochondrial DNA (mtDNA) displacement loop (D-loop) and a panel of nine nuclear microsatellite markers. A model constraining all clines to the same width and centre was not significantly different from a model in which the clines were allowed to vary independently. Locus-by-locus analysis indicated that the majority of nuclear clines shared the same centre as the mtDNA cline, and the widths of these clines were also narrower than that predicted by a neutral model, suggesting that selection is operating to maintain the hybrid zone. However, two of the nuclear clines had widths greater than the neutral prediction and had centres that were displaced relative to the mtDNA cline centre. We also found that a marsh located near the centre of the mtDNA cline demonstrated a bimodal distribution of nuclear hybrid index values, suggesting a deficit of first-generation hybrids and backcrossed genotypes. Thus, selection against hybrid genotypes may be playing a role in maintaining this hybrid zone and the associated steep nuclear and mtDNA clines.

Does hybridization with a widespread congener threaten the long-term persistence of the Eastern Alpine rare local endemic Knautia carinthiaca?

Interspecific hybridization, especially when regularly followed by backcrossing (i.e., introgressive hybridization), conveys a substantial risk for many endangered organisms. This is particularly true for narrow endemics occurring within distributional ranges of widespread congeners. An excellent example is provided by the plant genus Knautia (Caprifoliaceae): Locally endemic K. carinthiaca is reported from two isolated populations in southern Austria situated within an area predominantly occupied by widespread K. arvensis. While K. carinthiaca usually inhabits low-competition communities on rocky outcrops, K. arvensis occurs mainly in dry to mesic managed grasslands, yet both species can coexist in marginal environments and were suspected to hybridize. Flow cytometry revealed that diploid K. carinthiaca only occurs at its locus classicus, whereas the second locality is inhabited by the morphologically similar but tetraploid K. norica. In the, therefore, single population of K. carinthiaca, flow cytometry and AFLP fingerprinting showed signs of introgressive hybridization with diploid K. arvensis. Hybridization patterns were also reflected in intermediate habitat preferences and morphology of the hybrids. Environmental barriers to gene flow seem to prevent genetic erosion of K. carinthiaca individuals from the core ecological niches, restricting most introgressed individuals to peripheral habitats. Efficient conservation of K. carinthiaca will require strict protection of its habitat and ban on forest clear cuts in a buffer zone to prevent invasion of K. arvensis. We demonstrate the large potential of multidisciplinary approaches combining molecular, cytometric, and ecological tools for a reliable inventory and threat assessment of rare species.

Variation in the frequency and extent of hybridization between Leucosceptrum japonicum and L. stellipilum (Lamiaceae) in the Central Japanese Mainland

Variations in the frequency and extent of hybridization among mixed populations located in the same contact zone provide natural laboratories for the study of extrinsic reproductive isolation maintaining species integrity. In this study, we examined the pattern of hybridization between L. japonicum and L. stellipilum among mixed populations in different localities of a contact zone. The genetic structures from three sympatric populations and six mixed populations in the hybrid zone, and five reference populations far from the contact zone, were characterized using 10 neutral nuclear microsatellite markers. Evidence from genetic distance-based clustering analysis, the frequency distribution of admixture proportion values, and the hybrid category assignment approaches indicated that the frequency and extent of hybridization varied considerably among populations in the contact zone between L. japonicum and L. stellipilum. One likely explanation is that variation in exogenous (ecological) selection among populations might contribute to differences in frequency and extent of hybridization. The present study will facilitate future research exploring the evolution of reproductive isolation between L. japonicum and L. stellipilum.

Altitudinal gradients, plant hybrid zones and evolutionary novelty

Altitudinal gradients are characterized by steep changes of the physical and biotic environment that present challenges to plant adaptation throughout large parts of the world. Hybrid zones may form where related species inhabit different neighbouring altitudes and can facilitate interspecific gene flow and potentially the breakdown of species barriers. Studies of such hybrid zones can reveal much about the genetic basis of adaptation to environmental differences stemming from changes in altitude and the maintenance of species divergence in the face of gene flow. Furthermore, owing to recombination and transgressive effects, such hybrid zones can be sources of evolutionary novelty. We document plant hybrid zones associated with altitudinal gradients and emphasize similarities and differences in their structure. We then focus on recent studies of a hybrid zone between two Senecio species that occur at high and low altitude on Mount Etna, Sicily, showing how adaptation to local environments and intrinsic selection against hybrids act to maintain it. Finally, we consider the potential of altitudinal hybrid zones for generating evolutionary novelty through adaptive introgression and hybrid speciation. Examples of homoploid hybrid species of Senecio and Pinus that originated from altitudinal hybrid zones are discussed.

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.

Maintenance of strong morphological differentiation despite ongoing natural hybridization between sympatric species of Lomatia (Proteaceae)

BACKGROUND AND AIMS

When species cohesion is maintained despite ongoing natural hybridization, many questions are raised about the evolutionary processes operating in the species complex. This study examined the extensive natural hybridization between the Australian native shrubs Lomatia myricoides and L. silaifolia (Proteaceae). These species exhibit striking differences in morphology and ecological preferences, exceeding those found in most studies of hybridization to date.

METHODS

Nuclear microsatellite markers (nSSRs), genotyping methods and morphometric analyses were used to uncover patterns of hybridization and the role of gene flow in morphological differentiation between sympatric species.

KEY RESULTS

The complexity of hybridization patterns differed markedly between sites, however, signals of introgression were present at all sites. One site provided evidence of a large hybrid swarm and the likely presence of multiple hybrid generations and backcrosses, another site a handful of early generational hybrids and a third site only traces of admixture from a past hybridization event. The presence of cryptic hybrids and a pattern of morphological bimodality amongst hybrids often disguised the extent of underlying genetic admixture.

CONCLUSIONS

Distinct parental habitats and phenotypes are expected to form barriers that contribute to the rapid reversion of hybrid populations to their parental character state, due to limited opportunities for hybrid/intermediate advantage. Furthermore, strong genomic filters may facilitate continued gene flow between species without the danger of assimilation. Stochastic fire events facilitate temporal phenological isolation between species and may partly explain the bi-directional and site-specific patterns of hybridization observed. Furthermore, the findings suggest that F1 hybrids are rare, and backcrosses may occur rapidly following these initial hybridization events.

Nectar sugar composition of European Caryophylloideae (Caryophyllaceae) in relation to flower length, pollination biology and phylogeny

Floral nectar composition has been explained as an adaptation to factors that are either directly or indirectly related to pollinator attraction. However, it is often unclear whether the sugar composition is a direct adaptation to pollinator preferences. Firstly, the lower osmolality of sucrose solutions means that they evaporate more rapidly than hexose solutions, which might be one reason why sucrose-rich nectar is typically found in flowers with long tubes (adapted to long-tongued pollinators), where it is better protected from evaporation than in open or short-tubed flowers. Secondly, it can be assumed that temperature-dependent evaporation is generally lower during the night than during the day so that selection pressure to secrete nectar with high osmolality (i.e. hexose-rich solutions) is relaxed for night-active flowers pollinated at night. Thirdly, the breeding system may affect selection pressure on nectar traits; that is, for pollinator-independent, self-pollinated plants, a lower selective pressure on nectar traits can be assumed, leading to a higher variability of nectar sugar composition independent of pollinator preferences, nectar accessibility and nectar protection. To analyse the relations between flower tube length, day vs. night pollination and self-pollination, the nectar sugar composition was investigated in 78 European Caryophylloideae (Caryophyllaceae) with different pollination modes (diurnal, nocturnal, self-pollination) using high-performance liquid chromatography (HPLC). All Caryophylleae species (Dianthus and relatives) were found to have nectar with more than 50% sucrose, whereas the sugar composition of Sileneae species (Silene and relatives) ranged from 0% to 98.2%. In the genus Silene, a clear dichotomous distribution of sucrose- and hexose-dominant nectars is evident. We found a positive correlation between the flower tube length and sucrose content in Caryophylloideae, particularly in day-flowering species, using both conventional analyses and phylogenetically independent contrasts.

Introgressive hybridization between anciently diverged lineages of Silene (Caryophyllaceae)

Hybridization has played a major role during the evolution of angiosperms, mediating both gene flow between already distinct species and the formation of new species. Newly formed hybrids between distantly related taxa are often sterile. For this reason, interspecific crosses resulting in fertile hybrids have rarely been described to take place after more than a few million years after divergence. We describe here the traces of a reproductively successful hybrid between two ancestral species of Silene, diverged for about six million years prior to hybridization. No extant hybrids between the two parental lineages are currently known, but introgression of the RNA polymerase gene NRPA2 provides clear evidence of a temporary and fertile hybrid. Parsimony reconciliation between gene trees and the species tree, as well as consideration of clade ages, help exclude gene paralogy and lineage sorting as alternative hypotheses. This may represent one of the most extreme cases of divergence between species prior to introgressive hybridization discovered yet, notably at a homoploid level. Although species boundaries are generally believed to be stable after millions of years of divergence, we believe that this finding may indicate that gene flow between distantly related species is merely largely undetected at present.

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or both maternal species, (2) the sex-determining chromosome of the hybrid reflects the location of male sterility within the maternal donor species and (3) crosses from the hybrid species show less sexual dimorphism than the parental species. We found that F. × ananassa subsp. cuneifolia populations consisted of both parental cytotypes but one predominated within each population. Genetic linkage mapping of two crosses showed dominance of male sterility similar to the parental species, however, the map location of male sterility reflected the maternal donor in one cross, but not the other. Moreover, female function mapped to a single region in the first cross, but to two regions in the second cross. Aside from components of female function (fruit set and seed set), other traits that have been found to be significantly sexually dimorphic in the pure species were either not dimorphic or were dimorphic in the opposite direction to the parental species. These results suggest that hybrids experience some disruption of dimorphism in secondary sexual traits, as well as novel location and number of quantitative trait locus (QTL) affecting sex function.

Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae)

East Asia's temperate deciduous forests served as sanctuary for Tertiary relict trees, but their ages and response to past climate change remain largely unknown. To address this issue, we elucidated the evolutionary and population demographic history of Cercdiphyllum, comprising species in China/Japan (Cercdiphyllum japonicum) and central Japan (Cercdiphyllum magnificum). Fifty-three populations were genotyped using chloroplast and ribosomal DNA sequences and microsatellite loci to assess molecular structure and diversity in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modelling. Late Tertiary climate cooling was reflected in a relatively recent speciation event, dated at the Mio-/Pliocene boundary. During glacials, the warm-temperate C. japonicum experienced massive habitat losses in some areas (north-central China/north Japan) but increases in others (southwest/-east China, East China Sea landbridge, south Japan). In China, the Sichuan Basin and/or the middle-Yangtze were source areas of postglacial northward recolonization; in Japan, this may have been facilitated through introgressive hybridization with the cool-temperate C. magnificum. Our findings challenge the notion of relative evolutionary and demographic stability of Tertiary relict trees, and may serve as a guideline for assessing the impact of Neogene climate change on the evolution and distribution of East Asian temperate plants.

Identification of white campion (Silene latifolia) guaiacol O-methyltransferase involved in the biosynthesis of veratrole, a key volatile for pollinator attraction

BACKGROUND

Silene latifolia and its pollinator, the noctuid moth Hadena bicruris, represent an open nursery pollination system wherein floral volatiles, especially veratrole (1, 2-dimethoxybenzene), lilac aldehydes, and phenylacetaldehyde are of key importance for floral signaling. Despite the important role of floral scent in ensuring reproductive success in S. latifolia, the molecular basis of scent biosynthesis in this species has not yet been investigated.

RESULTS

We isolated two full-length cDNAs from S. latifolia that show similarity to rose orcinol O-methyltransferase. Biochemical analysis showed that both S. latifolia guaiacol O-methyltransferase1 (SlGOMT1) &S. latifolia guaiacol O-methyltransferase2 (SlGOMT2) encode proteins that catalyze the methylation of guaiacol to form veratrole. A large Km value difference between SlGOMT1 (~10 μM) and SlGOMT2 (~501 μM) resulted that SlGOMT1 is 31-fold more catalytically efficient than SlGOMT2. qRT-PCR expression analysis showed that the SlGOMT genes are specifically expressed in flowers and male S. latifolia flowers had 3- to 4-folds higher level of GOMT gene transcripts than female flower tissues. Two related cDNAs, S. dioica O-methyltransferase1 (SdOMT1) and S. dioica O-methyltransferase2 (SdOMT2), were also obtained from the sister species Silene dioica, but the proteins they encode did not methylate guaiacol, consistent with the lack of veratrole emission in the flowers of this species. Our evolutionary analysis uncovered that SlGOMT1 and SlGOMT2 genes evolved under positive selection, whereas SdOMT1 and SdOMT2 genes show no evidence for selection.

CONCLUSIONS

Altogether, we report the identification and functional characterization of the gene, SlGOMT1 that efficiently catalyzes veratrole formation, whereas another copy of this gene with only one amino acid difference, SlGOMT2 was found to be less efficient for veratrole synthesis in S. latifolia.

Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry

Closely related species coexisting in sympatry provide critical insight into the mechanisms underlying speciation and the maintenance of genetic divergence. Selfing may promote reproductive isolation by facilitating local adaptation, causing reduced hybrid fitness in parental environments. Here, we propose a novel mechanism by which selfing can further impair interspecific gene flow: selfing may act to ensure that nonhybrid progeny systematically co-occur whenever hybrid genotypes are produced. Under a competition arena, the fitness differentials between nonhybrid and hybrid progeny are then magnified, preventing development of interspecific hybrids. We investigate whether this "sibling competition arena" can explain the coexistence in sympatry of closely related species of the plant fungal pathogens (Microbotryum) causing anther-smut disease. The probabilities of intrapromycelial mating (automixis), outcrossing, and sibling competition were manipulated in artificial inoculations to evaluate their contribution to reproductive isolation. We report that both intrapromycelial selfing and sibling competition significantly reduced rates of hybrid infection beyond that expected based solely upon selfing rates and noncompetitive fitness differentials between hybrid and nonhybrid progeny. Our results thus suggest that selfing and a sibling competition arena can combine to constitute a barrier to gene flow and diminish selection for additional barriers to gene flow in sympatry.

Dynamics of drift, gene flow, and selection during speciation in Silene

The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F(ST)) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F(ST) can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F(ST), the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.

Differential response of the homoploid hybrid species Iris nelsonii (Iridaceae) and its progenitors to abiotic habitat conditions

PREMISE OF THE STUDY

Homoploid hybrid speciation involves the evolution of reproductive isolation between a hybrid lineage and its progenitors without a change in chromosome number. Ecological divergence presumably plays a large role in the stabilization of hybrid lineages, as all homoploid hybrid species described to date are reported to be ecologically divergent from their progenitors. However, the described ecological divergence in most systems is anecdotal and has not been empirically tested.

METHODS

We assessed the vegetative response of Iris nelsonii, a homoploid hybrid species, and its three progenitor species, I. brevicaulis, I. fulva, and I. hexagona, to different abiotic conditions (i.e., varied sunlight availability and flooding conditions) that largely characterize the habitats of these four species in their natural habitats in Louisiana, USA.

KEY RESULTS

The species differed in their responses to the water-level treatment for many of the response variables, including rhizome weight, ramet growth, plant height, and two principal components used to characterize the data. The species differed in their response to the light-level treatment for root allocation and the principal component used to characterize plant size. Iris nelsonii significantly differed from its progenitors, including its most closely related progenitor species, in response to many of the treatments.

CONCLUSIONS

The differential response to abiotic habitat conditions of I. nelsonii suggests that this species is ecologically divergent from its progenitor species.

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

BACKGROUND

The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database.

RESULTS

A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch.

CONCLUSION

The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.

Haldane's rule is extended to plants with sex chromosomes

Haldane's rule is an empirical phenomenon that has been observed in animals with sex chromosomes. The rule states that the heterogametic sex (XY or ZW) will be “absent, rare, or sterile” following hybridization between two species. Despite the near ubiquity of Haldane's rule in animal hybridizations, it has not been documented in organisms other than animals. Here, we show evidence for both rarity and sterility in hybrid male but not female offspring in crosses between three dioecious plant species from the genus Silene with heteromorphic (XY) sex chromosomes. Our results are consistent with Haldane's rule, extending its applicability to plants with sex chromosomes.

Disjunct distribution of chloroplast DNA haplotypes in the understory perennial Veratrum album ssp. oxysepalum (Melanthiaceae) in Japan as a result of ancient introgression

• The Quaternary climatic changes resulted in range shifts of species, providing chances for hybridization. However, the genetic signatures of such ancient introgression have rarely been reported. To investigate such signatures, we performed a phylogeographical study on the perennial plant Veratrum album ssp. oxysepalum, which may have hybridized long ago with another congeneric species, V. stamineum. • Sequence variations in chloroplast DNA (cpDNA) were examined in 43 populations in Japan and adjacent areas. Phylogenetic analyses of different cpDNA haplotypes were conducted on the basis of cpDNA and nuclear ribosomal internal transcribed spacer (nrITS) variations. • In the Japanese archipelago, two major groups of haplotypes were detected, one of which was distributed in a disjunct pattern. The major haplotype, occupying the central part of the species' distribution, formed a monophyletic group with V. stamineum in phylogenetic trees on the basis of cpDNA variation, although the two species did not form a monophyletic group in phylogenetic trees on the basis of nrITS variation. • Historical hybridization between V. album ssp. oxysepalum and V. stamineum in refugia during the Quaternary climatic oscillations, and the resulting chloroplast capture of V. stamineum by V. album ssp. oxysepalum, are most probably responsible for the disjunct distribution of cpDNA in V. album ssp. oxysepalum.

Unusual patterns of hybridization involving a narrow endemic Rhododendron species (Ericaceae) in Yunnan, China

PREMISE OF THE STUDY

One potential threat to rare species is genetic swamping caused by hybridization, but few studies have quantified this threat. Rhododendron cyanocarpum is a narrow endemic species that occurs sympatrically with potentially interfertile congeners throughout its range within Yunnan, China. We searched the entire distribution of R. cyanocarpum for hybrids and examined the patterns of hybridization to assess potential threat from hybridization. •

METHODS

In a comprehensive field survey, we detected only one instance of hybridization involving R. cyanocarpum, with R. delavayi, at Huadianba near Dali. Material of both species and putative hybrids was examined using morphology, chloroplast DNA, nuclear ribosomal DNA, and Bayesian analysis of AFLP profiles. •

KEY RESULTS

Of 10 putative hybrids, two were F(1)(')s and at least seven were F(2)(')s. Four backcrosses to R. delavayi were detected among material with R. delavayi-like morphology within the hybrid zone. Backcrosses to R. cyanocarpum were not detected. Therefore F(2)(')s outnumbered all other classes within the hybrid zone, a situation not previously confirmed for plants and extremely rare generally. Hybridization was asymmetrical, with R. delavayi as the maternal parent in all but one of the hybrids detected. •

CONCLUSIONS

Although natural hybridization is common in Rhododendron, it is rare in R. cyanocarpum and is apparently not accompanied by backcrossing toward R. cyanocarpum. Hence, there is no immediate risk of genetic swamping, unless habitat disturbance increases and changes the patterns of hybridization. Our study is the first to report a plant hybrid zone dominated by F(2) hybrids. This pattern might contribute to species barrier maintenance.