TEMPO AND MODE OF MATING SYSTEM EVOLUTION BETWEEN INCIPIENT CLARKIA SPECIES

The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system

Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability

Although selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of Mimulus guttatus for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species

The evolutionary transition from outcross- to self-fertilization is one of the most common in angiosperms and is often associated with a parallel shift in floral morphological and developmental traits, such as reduced flower size and pollen to ovule ratios, known as the "selfing syndrome." How these convergent phenotypes arise, the extent to which they are shaped by selection, and the nature of their underlying genetic basis are unsettled questions in evolutionary biology. The genus Collinsia (Plantaginaceae) includes seven independent transitions from outcrossing or mixed mating to high selfing rates accompanied by selfing syndrome traits. Accordingly, Collinsia represents an ideal system for investigating this parallelism, but requires genomic resource development. We present a high quality de novo genome assembly for the highly selfing species Collinsia rattanii. To begin addressing the basis of selfing syndrome developmental shifts, we evaluate and contrast patterns of gene expression from floral transcriptomes across three stages of bud development for C. rattanii and its outcrossing sister species Collinsia linearis. Relative to C. linearis, total gene expression is less variable among individuals and bud stages in C. rattanii. In addition, there is a common pattern among differentially expressed genes: lower expression levels that are more constant across bud development in C. rattanii relative to C. linearis. Transcriptional regulation of enzymes involved in pollen formation specifically in early bud development may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. Future work will include additional Collinsia outcrossing-selfing species pairs to identify genomic signatures of parallel evolution.

Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum

PREMISE

Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems.

METHODS

We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene.

RESULTS

Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico.

CONCLUSIONS

Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.

Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Are trait combinations facilitated, independent, or constrained?

PREMISE

Whether drought-adaptation mechanisms tend to evolve together, evolve independently, or evolve constrained by genetic architecture is incompletely resolved, particularly for water-relations traits besides gas exchange. We addressed this issue in two subspecies of Clarkia xantiana (Onagraceae), California winter annuals that separated approximately 65,000 years ago and are adapted, partly by differences in flowering time, to native ranges differing in precipitation.

METHODS

In these subspecies and in recombinant inbred lines (RILs) from a cross between them, we scored traits related to drought adaptation (timing of seed germination and of flowering, succulence, pressure-volume curve variables) in common environments.

RESULTS

The subspecies native to more arid environments (parviflora) exhibited slower seed germination in saturated conditions, earlier flowering, and greater succulence, likely indicating superior drought avoidance, drought escape, and dehydration resistance via water storage. The other subspecies (xantiana) had lower osmotic potential at full turgor and lower water potential at turgor loss, implying superior dehydration tolerance. Genetic correlations among RILs suggest facilitated evolution of some trait combinations and independence of others. Where genetic correlations exist, subspecies differences fell along them, with the exception of differences in succulence and turgor loss point. In that case, subspecies difference overcame genetic correlations, possibly reflecting strong selection and/or antagonistic genetic correlations with other traits.

CONCLUSIONS

Clarkia xantiana subspecies' differ in multiple mechanisms of drought adaptation. Genetic architecture generally does not seem to have constrained the evolution of these mechanisms, and it may have facilitated the evolution of some of trait combinations.

The opportunity for outcrossing varies across the geographic range of the primarily selfing Clarkia xantiana ssp. parviflora

PREMISE

The timing of self-fertilization has potentially important consequences for the trajectory of mating system evolution, the opportunity for outcrossing, and the maintenance of genetic variation in populations. For primarily selfing taxa, it remains poorly understood as to how floral variation influences the opportunity for outcrossing and whether those attributes vary among populations across geographic ranges.

METHODS

We examined variation in floral traits (herkogamy, protandry, flower size, stigma stage at anthesis, timing of stigma receptivity) in seven populations of Clarkia xantiana ssp. parviflora, a primarily selfing taxon, spanning from the western to eastern margins of its distribution. We also performed experimental emasculations and pollinations (followed by stigma severing) to quantify the extent of opportunities for outcrossing across flower development.

RESULTS

There was marked among-population variation in all floral traits, particularly between far eastern and western populations. Emasculation experiments showed that the eastern populations had minimal autonomous selfing, but western populations had high rates of selfing within 24 h after anthesis. Population variation in autofertility was significantly predicted by floral trait variation, especially protandry and petal size.

CONCLUSIONS

Greater protandry both extended the time over which outcrossing could potentially occur and reduced the probability of autonomous selfing, suggesting that there may be a tradeoff that results in fitness loss when pollinator visits are not common. The east-west pattern of differentiation in some floral traits parallels that of postglacial range expansion, suggesting that selection on the mating system may have been strong in the process of range expansion.

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.

Mating system impacts the genetic architecture of adaptation to heterogeneous environments

Self-fertilisation has consequences for variation across the genome as it reduces effective population size, effect recombination rates and pollen flow, with implications for local adaptation. We conducted simulations of divergent stabilising selection on a quantitative trait with drift, pollen flow, mutation, recombination and different outcrossing rates. We quantified trait divergence and the genetic architecture of adaptation. We conducted an F_ST outlier analysis to identify candidate loci and quantified the impact of mating system on detectability. Selfing promoted trait divergence mainly through reductions in pollen flow. Moreover, trait architecture became more diffuse with selfing. Average effect size of trait loci was lower, while the number of loci, and their clustering distance increased. The genetic architecture of selfers was also more diffuse than outcrossers for equivalent migration rates. However, when deleterious alleles were included, architectures became more concentrated in selfers, likely to be because of reductions in population size caused by mutational meltdown and impacts of background selection on N_e . Our simulations demonstrate that mating system has important impacts on adaptive divergence of traits and the genetic landscape underlying that divergence. Selfing has a significant effect on detectability of regions of the genome important for adaptation because of neutral divergence and diffuse trait architecture.

On the young age of intraspecific herbaceous taxa

Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.

Recent selection for self-compatibility in a population of Leavenworthia alabamica

The evolution of self-compatibility (SC) is the first step in the evolutionary transition in plants from outcrossing enforced by self-incompatibility (SI) to self-fertilization. In the Brassicaceae, SI is controlled by alleles of two tightly linked genes at the S-locus. Despite permitting inbreeding, mutations at the S-locus leading to SC may be selected if they provide reproductive assurance and/or gain a transmission advantage in a population when SC plants self- and outcross. Positive selection can leave a genomic signature in the regions physically linked to the focus of selection when selection has occurred recently. From an SC population of Leavenworthia alabamica with a known nonfunctional mutation at the S-locus, we collected sequence data from a ∼690 Kb region surrounding the S-locus, as well as from regions not linked to the S-locus. To test for recent positive selection acting at the S-locus, we examined polymorphism and the site-frequency spectra. Using forward simulations, we demonstrate that recent selection of the strength expected for SC at a locus formerly under balancing selection can generate patterns similar to those seen in our empirical data.

Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae)

PREMISE OF THE STUDY

The population biology of outcrossing and self-fertilizing taxa is thought to differ because of the advantage that selfers have in colonizing unoccupied sites where mates and pollinators may be limiting (Baker's Law). This reduced tendency for outcrossers to colonize new sites, along with their greater dependence on pollinators to disperse pollen, has the potential to differently influence the genetic diversity and structure of outcrossing and selfing populations.

METHODS

We conducted a comparative population genetic study of two sister outcrossing and selfing subspecies of Clarkia xantiana that have very recently diverged. We used DNA sequence variation (>40 kb from eight nuclear loci) from large samples of individuals from 14 populations to assess geographic patterns of genetic diversity and make inferences about the demographic and colonization histories of each subspecies.

KEY RESULTS

We show that sequence variation is strongly reduced across all selfing populations. The demographic history of selfing populations exhibits recent colonization bottlenecks, whereas such bottlenecks are rarely observed for the outcrosser. The greater effect of genetic drift in the selfer has resulted in strong population genetic structure, but with no pattern of isolation by distance. By contrast, the stronger effect of gene flow in the outcrosser has resulted in considerably less structure, but a significant pattern of isolation by distance.

CONCLUSIONS

Taken together, our results suggest that selfing populations are not at migration-drift equilibrium, are affected by strong episodes of genetic drift during colonization, and experience little or no subsequent gene flow from other populations after those founder events.

Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end

BACKGROUND

The transition from outcrossing to selfing has long been portrayed as an 'evolutionary dead end' because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a 'rostellum') co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing.

RESULTS

The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.4-3.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. ≤ 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing.

CONCLUSIONS

The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the 'rostellum') is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary (≤ 1.3 Ma) time scales.

The demography and population genomics of evolutionary transitions to self-fertilization in plants

The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae)

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Recurrent polymorphic mating type variation in Madagascan Bulbophyllum species (Orchidaceae) exemplifies a high incidence of auto-pollination in tropical orchids

The transition from outcrossing to self-fertilization is one of the most common evolutionary changes in angiosperms. The orchid family exemplifies this evolutionary trend but, because of a general lack of large-scale surveys on auto-pollination in orchid taxa, the incidence and modes of auto-pollination among (sub)tropical orchids remain poorly known. In the present study, we assessed the frequency and mode of auto-pollination within and among species of a largely monophyletic group of Madagascan Bulbophyllum. The capacity for autonomous fruit set was investigated by bagging experiments in the greenhouse and the field, complemented with detailed floral micromorphological studies of the gynostemium. Our survey comprises 393 accessions, representing at least 78 species, and thus approximately 37% of the species diversity of the genus in the Madagascan region. Our studies revealed that mating type is directly related to gynostemium structure, most often involving the presence or absence of a physical barrier termed 'rostellum'. As a novel and unexpected finding, we identified eight species of a single lineage of Madagascan Bulbophyllum (termed 'clade C'), in which auto-pollinating morphs (selfers), either lacking a rostellum or (rarely) possessing a stigmatic rostellum, co-exist with their pollinator-dependent conspecifics (outcrossers). We hypothesize that auto-pollination via rostellum abortion has a simple genetic basis, and probably evolved rapidly and recurrently by subtle changes in the timing of rostellum development (heterochrony). Thus, species of clade C may have an intrinsic genetic and developmental lability toward auto-pollination, allowing rapid evolutionary response under environmental, perhaps human-disturbed conditions favouring reproductive assurance. Overall, these findings should stimulate further research on the incidence, evolution, and maintenance of mating type variation in tropical orchids, as well as how they adapt(ed) to changing environmental conditions.

Limited genomic consequences of mixed mating in the recently derived sister species pair, Collinsia concolor and Collinsia parryi

Highly selfing species often show reduced effective population sizes and reduced selection efficacy. Whether mixed mating species, which produce both self and outcross progeny, show similar patterns of diversity and selection remains less clear. Examination of patterns of molecular evolution and levels of diversity in species with mixed mating systems can be particularly useful for investigating the relative importance of linked selection and demographic effects on diversity and the efficacy of selection, as the effects of linked selection should be minimal in mixed mating populations, although severe bottlenecks tied to founder events could still be frequent. To begin to address this gap, we assembled and analysed the transcriptomes of individuals from a recently diverged mixed mating sister species pair in the self-compatible genus, Collinsia. The de novo assembly of 52 and 37 Mbp C. concolor and C. parryi transcriptomes resulted in ~40 000 and ~55 000 contigs, respectively, both with an average contig size ~945. We observed a high ratio of shared polymorphisms to fixed differences in the species pair and minimal differences between species in the ratio of synonymous to replacement substitutions or codon usage bias implying comparable effective population sizes throughout species divergence. Our results suggest that differences in effective population size and selection efficacy in mixed mating taxa shortly after their divergence may be minimal and are likely influenced by fluctuating mating systems and population sizes.

Trait transitions in explicit ecological and genomic contexts: plant mating systems as case studies

Plants are astonishingly diverse in how they reproduce sexually, and the study of plant mating systems provides some of the most compelling cases of parallel and independent evolutionary transitions. In this chapter, we review how the massive amount of genomic data being produced is allowing long-standing predictions from ecological and evolutionary theory to be put to test. After a review of theoretical predictions about the importance of considering the genomic architecture of the mating system, we focus on a set of recent discoveries on how the mating system is controlled in a variety of model and non-model species. In parallel, genomic approaches have revealed the complex interaction between the evolution of genes controlling mating systems and genome evolution, both genome-wide and in the mating system control region. In several cases, major transitions in the mating system can be clearly associated with important ecological changes, hence illuminating an important interplay between ecological and genomic approaches. We also list a number of major unsolved questions that remain for the field, and highlight foreseeable conceptual developments that are likely to play a major role in our understanding of how plant mating systems evolve in Nature.

Evolutionary genetics of plant adaptation: insights from new model systems

Flowering time and mating system divergence are two of the most common adaptive transitions in plants. We review recent progress toward understanding the genetic basis of these adaptations in new model plant species. For flowering time, we find that individual crosses often reveal a simple genetic basis, but that the loci involved almost always vary within species and across environments, indicating a more complex genetic basis species-wide. Similarly, the transition to self-fertilization is often genetically complex, but this seems to depend on the amount of standing variation and time since species divergence. Recent population genomic studies also raise doubts about the long-term adaptive potential of self-fertilization, providing evidence that purifying selection is less effective in highly selfing species.

Floral specialization and angiosperm diversity: phenotypic divergence, fitness trade-offs and realized pollination accuracy

Plant reproduction by means of flowers has long been thought to promote the success and diversification of angiosperms. It remains unclear, however, how this success has come about. Do flowers, and their capacity to have specialized functions, increase speciation rates or decrease extinction rates? Is floral specialization fundamental or incidental to the diversification? Some studies suggest that the conclusions we draw about the role of flowers in the diversification and increased phenotypic disparity (phenotypic diversity) of angiosperms depends on the system. For orchids, for example, specialized pollination may have increased speciation rates, in part because in most orchids pollen is packed in discrete units so that pollination is precise enough to contribute to reproductive isolation. In most plants, however, granular pollen results in low realized pollination precision, and thus key innovations involving flowers more likely reflect reduced extinction rates combined with opportunities for evolution of greater phenotypic disparity (phenotypic diversity) and occupation of new niches. Understanding the causes and consequences of the evolution of specialized flowers requires knowledge of both the selective regimes and the potential fitness trade-offs in using more than one pollinator functional group. The study of floral function and flowering-plant diversification remains a vibrant evolutionary field. Application of new methods, from measuring natural selection to estimating speciation rates, holds much promise for improving our understanding of the relationship between floral specialization and evolutionary success.

Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia

BACKGROUND AND AIMS

Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement - that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies' range.

METHODS

Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology.

KEY RESULTS

Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction.

CONCLUSIONS

Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower size in sympatric parviflora (and RCD between parviflora and xantiana) is due to adaptation to limited pollinator availability. Rather, floral divergence appears to have been driven by other factors, such as interactions with congenerics in secondary sympatry.

Patterns of Selection in Plant Genomes

Plants show a wide range of variation in mating system, ploidy level, and demographic history, allowing for unique opportunities to investigate the evolutionary and genetic factors affecting genome-wide patterns of positive and negative selection. In this review, we highlight recent progress in our understanding of the extent and nature of selection on plant genomes. We discuss differences in selection as they relate to variation in demography, recombination, mating system, and ploidy. We focus on the population genetic consequences of these factors and argue that, although variation in the magnitude of purifying selection is well documented, quantifying rates of positive selection and disentangling the relative importance of recombination, demography, and ploidy are ongoing challenges. Large-scale comparative studies that examine the relative and joint importance of these processes, combined with explicit models of population history and selection, are key and feasible goals for future work.

Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella

The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the transition to self-fertilization.

While many plants require pollen from another individual to set seed, in some species self-pollination is the norm. This evolutionary shift from outcrossing to self-fertilization is among the most common transitions in flowering plants. Here, we use dense genome sequence data to identify where in the genome two individuals have inherited the same or different segments of ancestral diversity present in the founders of the selfing species, Capsella rubella to obtain a genome-wide view of this transition. This identification of founding haplotypes allows us to partition mutations into those that occurred before and after C. rubella separated from its outcrossing progenitor, C. grandiflora. With this partitioning, we estimate that C. rubella split from C. grandiflora between 50 and 100 kya. In this relatively short time frame, an extreme reduction in C. rubella's population size is associated with a massive loss of genetic variation and an increase in the relative proportion of putatively deleterious polymorphisms.

Resource reallocation does not influence estimates of pollen limitation or reproductive assurance in Clarkia xantiana subsp. parviflora (Onagraceae)

PREMISE OF STUDY

Studies of pollen limitation and the reproductive assurance value of selfing are important for examining the process of floral and mating system evolution in flowering plants. Recent meta-analyses have shown that common methods for measuring pollen limitation may often lead to biased estimates. Specifically, experiments involving single- or few-flower manipulations per plant tend to overestimate pollen limitation compared to those involving manipulations on most or all flowers per plant. Little previous work has explicitly tested for reallocation within individual systems using alternative methods and response variables. •

METHODS

We performed single-flower and whole-plant pollen supplementation and emasculation of flowers of Clarkia xantiana subsp. parviflora to estimate pollen limitation (PL) and reproductive assurance (RA). We compared levels of PL and RA using the following response variables: fruit set, seeds/flower, and seeds/plant. We also assessed the germination and viability of seeds to evaluate potential variation in pollen quality among treatments. •

KEY RESULTS

Autonomous selfing in Clarkia xantiana subsp. parviflora eliminates pollen limitation and provides reproductive assurance. Estimates from single-flower manipulations were not biased, closely resembling those from whole-plant manipulations. All three response variables followed the same pattern, but treatments were only significantly different for seeds/flower. Pollen quality, as indicated by seed viability, did not differ among treatments. •

CONCLUSIONS

Partial plant manipulations provided reliable estimates of pollen limitation and reproductive assurance. These estimates were also unaffected by accounting for pollen quality. Although whole plant manipulations are desirable, this experiment demonstrates that in some systems partial plant manipulations can be used in studies where whole-plant manipulations are not feasible.

Interactions of hybridization and mating systems: a case study in Leptosiphon (Polemoniaceae)

PREMISE OF THE STUDY

The roles of hybridization and mating systems in the evolution of angiosperms have been well studied, but less work has focused on their interactions. Self-incompatible and self-compatible species often show asymmetry in heterospecific pollen rejection. Self-fertilization can preempt ovules before opportunities for hybridization. In turn, hybridization might affect mating system evolution through selection for selfing to avoid production of low fitness hybrids. •

METHODS

AFLP and morphological analyses were used to test for hybrids in a contact zone between species with contrasting breeding systems. Crossing experiments examined the relative contributions to reproductive isolation of pollen-pistil interactions, timing of self-fertilization, and F1 viability and fertility. A diallel cross of siblings tested for an association between heterospecific incompatibility and S-genotype in the self-incompatible species. •

KEY RESULTS

A low frequency of hybrids was detected in the contact zone. Pollen-pistil interactions were partially consistent with the SI × SC rule; some individuals of the self-incompatible species rejected heterospecific pollen, whereas the self-compatible species was fully receptive to it. In the selfing species, individuals with early selfing produced fewer hybrid progeny than did those with delayed self-compatibility when heterospecific pollen was applied after self-pollen. Viability of F1s was high but fertility was low. Variability in heterospecific pollen rejection was not related to S-genotype. •

CONCLUSIONS

Both self-fertilization and self-incompatibility are associated with limits to hybridization at this site. The strong effect of timing of selfing on production of low fitness F1s suggests that hybridization might select for early selfing in this population.

Pollen Performance in Clarkia Taxa with Contrasting Mating Systems: Implications for Male Gametophytic Evolution in Selfers and Outcrossers

We tested three predictions regarding the joint evolution of pollen performance and mating system. First, due to the potential for intense intrasexual competition in outcrossing populations, we predicted that outcrossers would produce faster-growing pollen than their selfing relatives. Second, if elevated competition promotes stronger selection on traits that improve pollen performance, then, among-plant variation in pollen performance would be lower in outcrossers than in selfers. Third, given successive generations of adaptation to the same maternal genotype in selfers, we predicted that, in selfing populations (but not in outcrossing ones), pollen would perform better following self- than cross-pollinations. We tested these predictions in field populations of two pairs of Clarkia (Onagraceae) sister taxa. Consistent with our predictions, one outcrosser (C. unguiculata) exhibited faster pollen germination and less variation in pollen tube growth rate (PTGR) among pollen donors than its selfing sister species, C. exilis. Contrary to our predictions, the selfing C. xantiana ssp. parviflora exhibited faster PTGR than the outcrossing ssp. xantiana, and these taxa showed similar levels of variation in this trait. Pollen performance following self- vs. cross-pollinations did not differ within either selfing or outcrossing taxa. While these findings suggest that mating system and pollen performance may jointly evolve in Clarkia, other factors clearly contribute to pollen performance in natural populations.

Is self-fertilization an evolutionary dead end?

A compound hypothesis positing that self-fertilization is an evolutionary dead end conflates two distinct claims: the transition from outcrossing to selfing is unidirectional; and the diversification rate, or the balance of the speciation and extinction rate, is negative for selfing species. Both claims have enjoyed widespread informal support for decades, but have recently come under suspicion. Sources of data that apparently contradict strongly asymmetric mating system transitions often rely on statistical phylogenetic tests plagued by profound flaws. Although recently developed models mend preceding approaches, they have been employed sparingly, and many problems remain. Theoretical investigations, genetic data and applications of new phylogenetic methods provide indirect support for an association of selfing with negative diversification rates. We lack direct tests of reversals from selfing to outcrossing, and require data concerning the genetic basis and complexity of independently evolved outcrossing adaptations. The identification of the mechanisms that limit the longevity of selfing lineages has been difficult. Limitations may include brief and variable durations of selfing lineages, as well as ongoing difficulties in relating additive genetic and nucleotide variation. Furthermore, a common line of evidence for the stability of mixed mating - based simply on its frequent occurrence - is misleading. We make specific suggestions for research programs that aim to provide a richer understanding of mating system evolution and seriously challenge Stebbins' venerable hypothesis.

Comparative population genomics in Collinsia sister species reveals evidence for reduced effective population size, relaxed selection, and evolution of biased gene conversion with an ongoing mating system shift

Selfing species experience reduced effective recombination rates and effective population size, which can lead to reductions in polymorphism and the efficacy of natural selection. Here, we use illumina transcriptome sequencing and population resequencing to test for changes in polymorphism, base composition, and selection in the selfing angiosperm Collinsia rattanii (Plantaginaceae) compared with its more outcrossing sister species Collinsia linearis. Coalescent analysis indicates intermediate species divergence (500,000-1 million years) with no ongoing gene flow, but also evidence that the C. rattanii clade remains polymorphic for floral morphology and mating system, suggesting either an ongoing shift to selfing or a potential reversal from selfing to outcrossing. We identify a significant reduction in polymorphism in C. rattanii, particularly within populations. Analysis of polymorphisms suggests an elevated ratio of unique nonsynonymous to synonymous polymorphism in C. rattanii, consistent with relaxed selection in selfing lineages. We additionally find higher linkage disequilibrium and differentiation, lower GC content at variable sites, and reduced expression of genes important in pollen production and pollinator attraction in C. rattanii compared with C. linearis. Together, our results highlight the potential for rapid shifts in the efficacy of selection, gene expression and base composition associated with ongoing evolution of selfing.

Tempo and mode in plant breeding system evolution

Classic questions about trait evolution-including the directionality of character change and its interactions with lineage diversification-intersect in the study of plant breeding systems. Transitions from self-incompatibility to self-compatibility are frequent, and they may proceed within a species ("anagenetic" mode of breeding system change) or in conjunction with speciation events ("cladogenetic" mode of change). We apply a recently developed phylogenetic model to the nightshade family Solanaceae, quantifying the relative contributions of these two modes of evolution along with the tempo of breeding system change, speciation, and extinction. We find that self-incompatibility, a genetic mechanism that prevents self-fertilization, is lost largely by the cladogenetic mode. Self-compatible species are thus more likely to arise from the isolation of a newly self-compatible population than from species-wide fixation of self-compatible mutants. Shared polymorphism at the locus that governs self-incompatibility shows it to be ancestral and not regained within this family. We demonstrate that failing to account for cladogenetic character change misleads phylogenetic tests of evolutionary irreversibility, both for breeding system in Solanaceae and on simulated trees.