Studying flowers in 3D using photogrammetry

Flowers are intricate and integrated three-dimensional (3D) structures predominantly studied in 2D due to the difficulty in quantitatively characterising their morphology in 3D. Given the recent development of analytical methods for high-dimensional data, the reconstruction of flower models in three dimensions represents the limiting factor to studying flowers in 3D. We developed a floral photogrammetry protocol to reconstruct 3D models of flowers based on images taken with a digital single-lens reflex camera, a turntable and a portable lightbox. We demonstrate that photogrammetry allows a rapid and accurate reconstruction of 3D models of flowers from 2D images. It can reconstruct all visible parts of flowers and has the advantage of keeping colour information. We illustrated its use by studying the shape and colour of 18 Gesneriaceae species. Photogrammetry is an affordable alternative to micro-computed tomography (micro-CT) that requires minimal investment and equipment, allowing it to be used directly in the field. It has the potential to stimulate research on the evolution and ecology of flowers by providing a simple way to access 3D morphological data from a variety of flower types.

Self-incompatibility and the genetic architecture of inbreeding depression

Inbreeding depression plays a fundamental role in evolution. To help detect and characterize the loci that underlie inbreeding depression, we used bud pollination and salt treatments to circumvent self-incompatibility (SI) in plants from populations of Leavenworthia alabamica and produced families of progeny that were then genotyped at genetically mapped single-nucleotide polymorphism (SNP) loci. Using Bayesian inference, the segregation patterns for each SNP were used to explore support for different dominance and selection coefficients at linked viability loci in different genomic regions. There was support for several partially recessive viability loci in one of the populations, and one such locus mapped to the genomic region of the novel SI locus in L. alabamica. These results are consistent with earlier findings that showed purging of inbreeding depression for germination rate in L. alabamica. They are also consistent with expectations from evolutionary genetic theory that recessive, deleterious alleles linked to loci under balancing selection can be sheltered from selection.

The Evolutionary Forces Shaping Cis- and Trans-Regulation of Gene Expression within a Population of Outcrossing Plants

Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route toward achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and stronger negative selection acting on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans-regulation.

Somatic Mutation and Evolution in Plants

Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.

Inbreeding depression is difficult to purge in self-incompatible populations of Leavenworthia alabamica

The extent to which inbreeding depression can be purged is a major determinant of mating system evolution and is important to conservation and crop improvement. Studies of inbreeding depression purging have not been conducted in self-incompatible plants before. An experimental ('ancestral') treatment was first created from self-incompatible plants of Leavenworthia alabamica. Lines derived from this population were maintained by self-pollination for three generations in the attempt to create a 'purged' population with fewer recessive, deleterious mutations of large effect. Fitness components and the frequency of malformed phenotypes were monitored in progeny derived from selfing and outcrossing in the ancestral and purged treatments. Fitness component means and inbreeding depression were largely unchanged by three generations of forced self-pollination, and there was no reduction in the frequency of plants exhibiting malformed phenotypes. Our findings indicate that inbreeding depression in this species is largely a result of mutations of mild effect, consistent with the observation that self-incompatibility is maintained in most populations of L. alabamica, despite the presence of genetic variants with weaker self-incompatibility. Moreover, although population theory suggests that deleterious mutations of large effect should be sheltered from selection in the region of self-incompatibility locus, our results do not support this prediction.

The Contemporary Evolution of Fitness

The rate of evolution of population mean fitness informs how selection acting in contemporary populations can counteract environmental change and genetic degradation (mutation, gene flow, drift, recombination). This rate influences population increases (e.g., range expansion), population stability (e.g., cryptic eco-evolutionary dynamics), and population recovery (i.e., evolutionary rescue). We review approaches for estimating such rates, especially in wild populations. We then review empirical estimates derived from two approaches: mutation accumulation (MA) and additive genetic variance in fitness (IAw). MA studies inform how selection counters genetic degradation arising from deleterious mutations, typically generating estimates of <1% per generation. IAw studies provide an integrated prediction of proportional change per generation, nearly always generating estimates of <20% and, more typically, <10%. Overall, considerable, but not unlimited, evolutionary potential exists in populations facing detrimental environmental or genetic change. However, further studies with diverse methods and species are required for more robust and general insights.

The unusual S locus of Leavenworthia is composed of two sets of paralogous loci

The Leavenworthia self-incompatibility locus (S locus) consists of paralogs (Lal2, SCRL) of the canonical Brassicaceae S locus genes (SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear. BAC cloning and expression analyses were employed to characterize these SRK-like sequences. An SRK-positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/SCR haplotype is functional in self-incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles. An ancestral translocation or recombination event involving SRK/SCR and Lal2/SCRL likely occurred, together with neofunctionalization of Lal2/SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins.

Transitions from distyly to homostyly are associated with floral evolution in the buckwheat genus (Fagopyrum)

PREMISE OF THE STUDY

Documenting trait transitions among species with dimorphic flowers can help to test whether similar patterns of selection are responsible for divergence in floral traits among different species. Heterostyly is thought to promote outcrossing. Theory suggests that the evolutionary transition from heterostylous to homostylous flowers should be accompanied by a reduction in floral size in which pollen size and style length are expected to covary. Patterns of such correlated floral trait evolution have not, however, been widely examined.

METHODS

The evolutionary history of heterostyly and homostyly was reconstructed from a molecular phylogeny of 13 species of Fagopyrum and two outgroups, based on one nuclear gene (nrITS) and three chloroplast regions (matK, atpB-rbcL, and psbA-trnH spacer). Floral traits of nine Fagopyrum species including pollen number and size, as well as stigma depth (length of the capitate stigma), were measured and ancestral characters of the herkogamic condition were reconstructed.

KEY RESULTS

Three transitions from distyly to homostyly were observed. In two transitions, flower size (corolla diameter, pedicel length), herkogamy (stigma-anther distance) and pollen production decreased, but stigma depth and pollen size did not. Changes of anther height and style length were inconsistent. The predicted positive relationship between style length and pollen size in the two transitions to homostyly was not observed.

CONCLUSIONS

Floral evolution accompanying transitions to homostyly in Fagopyrum were found to be consistent with predictions of mating system evolution theory, and the correlation of traits in distylous vs. homostylous species revealed that pollen size generally correlates with stigma depth rather than style length.

PATTERN OF PHENOTYPIC VIABILITY AND FECUNDITY SELECTION IN A NATURAL POPULATION OF IMPATIENS PALLIDA

Estimates of viability and fecundity selection of 13 phenotypic characters for 1,536 individuals of Impatiens pallida growing in 24 locations within a single natural population were compared. Directional viability selection of cotyledon area, day of initial leaf production, number of leaves, and stem length was detected throughout this population. Directional fecundity selection of cotyledon area, day of initial flower production, number of leaves present on day of initial flower production, stem length on day of initial flower production, number of leaves, and stem length was also detected. Phenotypic selection of these characters was strong in some cases, and the strength of selection was significantly heterogeneous among locations. For several of the characters, directional phenotypic selection within the population was significantly positive in some locations and significantly negative in others separated by only a few meters. Fecundity selection was stronger than viability selection for some characters, implying that fecundity selection was at least as important as viability selection within this population. Soil moisture levels and light intensities played a larger role than soil nutrient levels in determining the patterns of both viability and fecundity selection, and differences in directional viability selection were more strongly related to environmental variation than were differences in fecundity selection. The pattern of phenotypic selection could not be reliably inferred from the patterns of mortality and reproduction alone.

WHOLE- AND PART-FLOWER SELF-POLLINATION IN GLYCINE CLANDESTINA AND G. ARGYREA AND THE EVOLUTION OF AUTOGAMY

The overall rate of self-fertilization can be viewed as the sum of two distinct processes: 1) self-pollination of all ovules in a flower (whole-flower self-pollination); and 2) self-pollination of some of the ovules in a flower, occurring together with outcrossing of the remaining ovules (part-flower self-pollination). In some situations these processes may be equated with different modes of self-pollination. A model of the mating system in which the progeny of separate fruits serve as the unit of observation is presented. The model partitions the overall rate of self-pollination into components attributable to whole- and part-flower selfing. When the mating system is estimated using information on marker genotypes from chasmogamous fruits in two species of Glycine together with the whole- and part-flower selfing model, the results indicate that the chasmogamous flowers in a subalpine population of G. clandestina underwent a significant level of whole-flower selfing, whereas in another, lower elevation population of G. clandestina and in a subtropical population of G. argyrea, they did not. This difference is thought to be related to the contrast in the variability of environmental conditions for insect-mediated pollination between the habitats sampled. In particular, the large component of whole-flower selfing observed in the subalpine population of G. clandestina may be due to self-pollination that is induced during periods unfavorable to insect-mediated pollination. It can be demonstrated that such induced selfing will be selected whenever environmental conditions are such that pollinator activity limits seed set, and moreover that induced selfing can result in the selection of overall levels of self-pollination that are intermediate between 0 and 1. Monte Carlo simulation is employed to show that ignoring the correlation of self-fertilization events that result from whole- and part-flower selfing may lead to biased estimates of mating system parameters.

EVOLUTIONARY HISTORY OF THE MATING SYSTEM IN AMSINCKIA (BORAGINACEAE)

A survey of restriction site variation in the chloroplast genome of the annual plant genus Amsinckia, together with estimation of outcrossing rates, was conducted to analyze the evolutionary history of the mating system. Species, and in some cases populations within species, differ markedly in their mating system. Five taxa are distylous and predominantly outcrossing, or show mixed mating systems, while the remaining taxa are homostylous and predominantly self-fertilizing. Reconstruction of the molecular phylogeny of the group places different distylous and homostylous taxa at four separate branch tips. When distyly is treated as ancestral in the group, or when the loss of distyly is assumed to be more common than its gain, the results of the phylogenetic analysis support the hypothesis that the self-fertilizing taxa are of recent origin from outcrossing relatives. These findings are discussed with respect to theory for the evolution and breakdown of distyly and the probability of extinction of selfing lineages.

The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora

Interactions between genes can have important consequences for how selection shapes sequence variation at these genes. Specifically, genes that have pleiotropic effects by affecting the expression level of many other genes may be under stronger selective constraint. We used coexpression networks to measure connectivity between genes and investigated the relationship between gene connectivity and selection in a natural population of the plant Capsella grandiflora. We observed that network connectivity was negatively correlated with genetic divergence due to stronger negative selection on highly-connected genes even when controlling for variation in gene expression level. However, the presence of local regulatory variation for a gene's expression level was also associated with reduced negative selection and lower gene connectivity. While it is difficult to disentangle the causal relationships between these factors, our results show that both connectivity and local regulatory variation are important factors for explaining variation in selection between genes.

Genetic variation for pseudo-self-compatibility in self-incompatible populations of Leavenworthia alabamica (Brassicaceae)

Self-incompatibility (SI) promotes outcrossing, but transitions to self-compatibility (SC) are frequent. Population genetic theory describing the breakdown of SI to SC suggests that, under most conditions, populations should be composed of either SI or SC individuals. Under a narrow range of conditions, theory suggests that SI may persist alongside reduced expression of SI (pseudo-SI, PSI) in mixed-mating populations. We studied genetic variation for PSI segregating in four SI populations of Leavenworthia alabamica by measurement of the heritability of pollen tube number after self-pollination. We tested for the role of the S-locus in this variation by sequencing seven S-alleles from plants with high pseudo-SC (PSC) and testing for the co-segregation of these alleles with PSC. We found a continuous distribution of PSC in all populations and 90% of plants exhibited PSC. The heritability ranged from 0.39 to 0.57. All seven S-alleles from plants with high PSC exhibited trans-specific polymorphism, and no stop codons were observed within the c. 600-bp region sequenced. One of these S-alleles was directly associated with the inheritance of PSC. We conclude that heritable variation in PSC is largely a result of genetic variation in the signaling cascade downstream of the S-locus reaction, together with the presence of one leaky S-allele.

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.

Selection of sporophytic and gametophytic self-incompatibility in the absence of a superlocus

Self-incompatibility (SI) is a complex trait that enforces outcrossing in plant populations. SI generally involves tight linkage of genes coding for the proteins that underlie self-pollen detection and pollen identity specification. Here, we develop two-locus genetic models to address the question of whether sporophytic SI (SSI) and gametophytic SI (GSI) can invade populations of self-compatible plants when there is no linkage or weak linkage of the underlying pollen detection and identity genes (i.e., no S-locus supergene). The models assume that SI evolves as a result of exaptation of genes formerly involved in functions other than SI. Model analysis reveals that SSI and GSI can invade populations even when the underlying genes are loosely linked, provided that inbreeding depression and selfing rate are sufficiently high. Reducing recombination between these genes makes conditions for invasion more lenient. These results can help account for multiple, independent evolution of SI systems as seems to have occurred in the angiosperms.

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

Somatic deleterious mutation rate in a woody plant: estimation from phenotypic data

We conducted controlled crosses in populations of the long-lived clonal shrub, Vaccinium angustifolium (lowbush blueberry) to estimate inbreeding depression and mutation parameters associated with somatic deleterious mutation. Inbreeding depression level was high, with many plants failing to set fruit after self-pollination. We also compared fruit set from autogamous pollinations (pollen collected from within the same inflorescence) with fruit set from geitonogamous pollinations (pollen collected from the same plant but from inflorescences separated by several meters of branch growth). The difference between geitonogamous versus autogamous fitness within single plants is referred to as 'autogamy depression' (AD). AD can be caused by somatic deleterious mutation. AD was significantly different from zero for fruit set. We developed a maximum-likelihood procedure to estimate somatic mutation parameters from AD, and applied it to geitonogamous and autogamous fruit set data from this experiment. We infer that, on average, approximately three sublethal, partially dominant somatic mutations exist within the crowns of the plants studied. We conclude that somatic mutation in this woody plant results in an overall genomic deleterious mutation rate that exceeds the rate measured to date for annual plants. Some implications of this result for evolutionary biology and agriculture are discussed.

Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia

Self-incompatibility (SI) is the flowering plant reproductive system in which self pollen tube growth is inhibited, thereby preventing self-fertilization. SI has evolved independently in several different flowering plant lineages. In all Brassicaceae species in which the molecular basis of SI has been investigated in detail, the product of the S-locus receptor kinase (SRK) gene functions as receptor in the initial step of the self pollen-rejection pathway, while that of the S-locus cysteine-rich (SCR) gene functions as ligand. Here we examine the hypothesis that the S locus in the Brassicaceae genus Leavenworthia is paralogous with the S locus previously characterized in other members of the family. We also test the hypothesis that self-compatibility in this group is based on disruption of the pollen ligand-producing gene. Sequence analysis of the S-locus genes in Leavenworthia, phylogeny of S alleles, gene expression patterns, and comparative genomics analyses provide support for both hypotheses. Of special interest are two genes located in a non-S locus genomic region of Arabidopsis lyrata that exhibit domain structures, sequences, and phylogenetic histories similar to those of the S-locus genes in Leavenworthia, and that also share synteny with these genes. These A. lyrata genes resemble those comprising the A. lyrata S locus, but they do not function in self-recognition. Moreover, they appear to belong to a lineage that diverged from the ancestral Brassicaceae S-locus genes before allelic diversification at the S locus. We hypothesize that there has been neo-functionalization of these S-locus-like genes in the Leavenworthia lineage, resulting in evolution of a separate ligand-receptor system of SI. Our results also provide support for theoretical models that predict that the least constrained pathway to the evolution of self-compatibility is one involving loss of pollen gene function.

Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia

Self-incompatibility (SI) is the flowering plant reproductive system in which self pollen tube growth is inhibited, thereby preventing self-fertilization. SI has evolved independently in several different flowering plant lineages. In all Brassicaceae species in which the molecular basis of SI has been investigated in detail, the product of the S-locus receptor kinase (SRK) gene functions as receptor in the initial step of the self pollen-rejection pathway, while that of the S-locus cysteine-rich (SCR) gene functions as ligand. Here we examine the hypothesis that the S locus in the Brassicaceae genus Leavenworthia is paralogous with the S locus previously characterized in other members of the family. We also test the hypothesis that self-compatibility in this group is based on disruption of the pollen ligand-producing gene. Sequence analysis of the S-locus genes in Leavenworthia, phylogeny of S alleles, gene expression patterns, and comparative genomics analyses provide support for both hypotheses. Of special interest are two genes located in a non-S locus genomic region of Arabidopsis lyrata that exhibit domain structures, sequences, and phylogenetic histories similar to those of the S-locus genes in Leavenworthia, and that also share synteny with these genes. These A. lyrata genes resemble those comprising the A. lyrata S locus, but they do not function in self-recognition. Moreover, they appear to belong to a lineage that diverged from the ancestral Brassicaceae S-locus genes before allelic diversification at the S locus. We hypothesize that there has been neo-functionalization of these S-locus-like genes in the Leavenworthia lineage, resulting in evolution of a separate ligand-receptor system of SI. Our results also provide support for theoretical models that predict that the least constrained pathway to the evolution of self-compatibility is one involving loss of pollen gene function.

Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia

Self-incompatibility (SI) is the flowering plant reproductive system in which self pollen tube growth is inhibited, thereby preventing self-fertilization. SI has evolved independently in several different flowering plant lineages. In all Brassicaceae species in which the molecular basis of SI has been investigated in detail, the product of the S-locus receptor kinase (SRK) gene functions as receptor in the initial step of the self pollen-rejection pathway, while that of the S-locus cysteine-rich (SCR) gene functions as ligand. Here we examine the hypothesis that the S locus in the Brassicaceae genus Leavenworthia is paralogous with the S locus previously characterized in other members of the family. We also test the hypothesis that self-compatibility in this group is based on disruption of the pollen ligand-producing gene. Sequence analysis of the S-locus genes in Leavenworthia, phylogeny of S alleles, gene expression patterns, and comparative genomics analyses provide support for both hypotheses. Of special interest are two genes located in a non-S locus genomic region of Arabidopsis lyrata that exhibit domain structures, sequences, and phylogenetic histories similar to those of the S-locus genes in Leavenworthia, and that also share synteny with these genes. These A. lyrata genes resemble those comprising the A. lyrata S locus, but they do not function in self-recognition. Moreover, they appear to belong to a lineage that diverged from the ancestral Brassicaceae S-locus genes before allelic diversification at the S locus. We hypothesize that there has been neo-functionalization of these S-locus-like genes in the Leavenworthia lineage, resulting in evolution of a separate ligand-receptor system of SI. Our results also provide support for theoretical models that predict that the least constrained pathway to the evolution of self-compatibility is one involving loss of pollen gene function.

The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley

Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant-pathogen co-evolution in wild systems.

Demographic signatures accompanying the evolution of selfing in Leavenworthia alabamica

The evolution of selfing from outcrossing is a common transition, yet little is known about the mutations and selective factors that promote this shift. In the mustard family, single-locus self-incompatibility (SI) enforces outcrossing. In this study, we test whether mutations causing self-compatibility (SC) are linked to the self-incompatibility locus (S-locus) in Leavenworthia alabamica, a species where two selfing races (a2 and a4) co-occur with outcrossing populations. We also infer the ecological circumstances associated with origins of selfing using molecular sequence data. Genealogical reconstruction of the Lal2 locus, the putative ortholog of the SRK locus, showed that both selfing races are fixed for one of two different S-linked Lal2 sequences, whereas outcrossing populations harbor many S-alleles. Hybrid crosses demonstrated that S-linked mutations cause SC in each selfing race. These results strongly suggest two origins of selfing in this species, a result supported by population admixture analysis of 16 microsatellite loci and by a population tree built from eight nuclear loci. One selfing race (a4) shows signs of a severe population bottleneck, suggesting that reproductive assurance might have caused the evolution of selfing in this case. In contrast, the population size of race a2 cannot be distinguished from that of outcrossing populations after correcting for differences in selfing rates. Coalescent-based analyses suggest a relatively old origin of selfing in the a4 race (∼150 ka ago), whereas selfing evolved recently in the a2 race (∼12-48 ka ago). These results imply that S-locus mutations have triggered two recent shifts to selfing in L. alabamica, but that these transitions are not always associated with a severe population bottleneck, suggesting that factors other than reproductive assurance may play a role in its evolution.

Estimation of mating system parameters when outcrossing events are correlated

Many plant species have mating systems characterized by a mixture of self-fertilization and outcrossing. Statistical estimation of the outcrossing rate has relied on a model of the mating process that assumes that successive outcross events within a family arise from independent draws of pollen from the total population of male plants. Although this assumption is likely to be most appropriate for wind-pollinated plants, it is not appropriate in certain insect-pollinated plants. An alternative model is developed that assumes that successive outcross events within a family involve pollen drawn from a single male parent. The estimation of the parameters that index this model is outlined and a procedure for calculating the variances of the parameter estimates is presented. Monte Carlo simulations of the sampling processes assumed by each model are also presented. The simulations show that application of the incorrect estimation model to data can lead to a large bias in parameter estimates.

The evolution of self-fertilization in perennials

Many plants are perennials, but studies of self-fertilization do not usually include features of perennial life histories. We therefore develop models that include selfing, a simple form of perenniality, adult inbreeding depression, and an adult survivorship cost to seed production. Our analysis shows that inbreeding depression in adults diminishes the genetic transmission advantage associated with selfing, especially in long-lived perennials that experience inbreeding depression over many seasons. Perennials also pay a cost when selfing increases total seed set at the expense of future survivorship and reproduction. Such life-history considerations shed new light on the generalization that annuals self-fertilize more than perennials. Past research suggested reproductive assurance as an explanation for this association, but common modes of selfing offer equal reproductive assurance to annuals and perennials. Instead, perennials may avoid selfing because of adult inbreeding depression and the cost to future survivorship and reproduction.

The evolution of self-incompatibility when mates are limiting

Self-incompatibility (SI) is a genetic barrier to inbreeding that is broadly distributed in angiosperms. In finite populations of SI plants, the loss of S-allele diversity can limit plant reproduction by reducing the availability of compatible mates. Many studies have shown that small or fragmented plant populations suffer from mate limitation. The advent of molecular typing of S-alleles in many species has paved the way to address quantitatively the importance of mate limitation, and to provide greater insight into why and how SI systems breakdown frequently in nature. In this review, we highlight the ecological factors that contribute to mate limitation in SI taxa, discuss their consequences for the evolution and functioning of SI, and propose new empirical research directions.

Transposable elements, mutational correlations, and population divergence in Caenorhabditis elegans

Transposable element activity is thought to be responsible for a large portion of all mutations, but its influence on the evolution of populations has not been well studied. Using mutation accumulation experiments with the nematode Caenorhabditis elegans, we investigated the impact of transposable element activity on the production of mutational variances and covariances. The experiments involved the use of two mutator strains (RNAi-deficient mutants) that are characterized by high levels of germline transposition, as well as the Bristol N2 strain, which lacks germline transposition. We found that transposition led to an increase in mutational heritabilities, as well as to the intensification of correlation patterns observed in the absence of transposition. No mutational trade-offs were detected and mutations generally had a deleterious effect on components of fitness. We also tested whether the pattern of mutational covariation could be used to predict observed patterns of population divergence in this species. Using 15 natural populations, we found that population divergence of C. elegans in multivariate phenotypic space occurred in directions only partially concordant with mutation, and thus other evolutionary factors, such as natural selection and genetic drift, must be acting to produce divergence within this species. Our results suggest that mutations induced by mobile elements in C. elegans are similar to other spontaneous mutations with respect to their contribution to the microevolution of quantitative traits.

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.

Low impact of germline transposition on the rate of mildly deleterious mutation in Caenorhabditis elegans

Little is known about the role of transposable element (TE) insertion in the production of mutations with mild effects on fitness, the class of mutations thought to be central to the evolution of many basic features of natural populations. We propagated mutation-accumulation (MA) lines of two RNAi-deficient strains of Caenorhabditis elegans that exhibit germline transposition. We show here that the impact of TE activity was to raise the level of mildly deleterious mutation by 2- to 8.5-fold, as estimated from fecundity, longevity, and body length measurements, compared to that observed in a parallel MA experiment with a control strain characterized by a lack of germline transposition. Despite this increase, the rate of mildly deleterious mutation was between one and two orders of magnitude lower than the rate of TE accumulation, which was approximately two new insertions per genome per generation. This study suggests that high rates of TE activity do not necessarily translate into high rates of detectable nonlethal mutation.

Retrotransposon Sequence Variation in Four Asexual Plant Species

Transposable elements (TEs) can be viewed as genetic parasites that persist in populations due to their capacity for increase in copy number and the inefficacy of selection against them. A corollary of this hypothesis is that TEs are more likely to spread within sexual populations and be eliminated or inactivated within asexual populations. While previous work with animals has shown that asexual taxa may contain less TE diversity than sexual taxa, comparable work with plants has been lacking. Here we report the results of a study of Ty1/copia, Ty3/gypsy, and LINE-like retroelement diversity in four asexual plant species. Retroelement-like sequences, with a high degree of conservation both within and between species, were isolated from all four species. The sequences correspond to several previously annotated retroelement subfamilies. They also exhibit a pattern of nucleotide substitution characterized by an excess of synonymous substitutions, suggestive of a history of purifying selection. These findings were compared with retroelement sequence evolution in sexual plant taxa. One likely explanation for the discovery of conserved TE sequences in the genomes of these asexual taxa is simply that asexuality within these taxa evolved relatively recently, such that the loss and breakdown of TEs is not yet detectable through analysis of sequence diversity. This explanation is examined by conducting stochastic simulation of TE evolution and by using published information to infer rough estimates of the ages of asexual taxa.

Deleterious mutation in related species of the plant genus Amsinckia with contrasting mating systems

Theory for the evolution of modifiers of the rate of mutation suggests that a lower rate of mutation may evolve after the breakdown of mechanisms that enforce outcrossing. Mutation accumulation (MA) experiments were conducted to compare deleterious mutation parameters in two closely related species of the plant genus Amsinckia, a group that exhibits wide variation in the mating system. One of the two species studied (A. douglasiana) is predominantly outcrossed in natural populations, where as the other species (A. gloriosa) is predominantly self-pollinated. Progeny assays of flower number per plant from generation 1 lines (control) and generation 11 lines (MA treatment) were conducted in both species. Dry weight measurements of progeny from the control and MA treatment in A. douglasiana also were made. Estimation of mutation parameters was conducted using maximum likelihood under the assumption of a gamma distribution of mutational effects. The two species exhibited similar rates and effects of deleterious mutation affecting flower number. Estimates of mutation rate for dry weight in A. douglasiana are close to those for flower number. Overall, the estimates of mutation parameters observed in these species are intermediate within the range reported for fitness components in other eukaryotes. The results are discussed within the context of evolutionary change in deleterious mutation accompanying mating system evolution and with respect to previous estimates of mutation parameters based on assays of inbreeding depression and the assumption of mutation-selection equilibrium.

Genomic mutation in lines of Arabidopsis thaliana exposed to ultraviolet-B radiation

Studies that have attempted to estimate the rate of deleterious mutation have typically been conducted under low levels of ultraviolet-B (UV-B) radiation, a naturally occurring mutagen. We conducted experiments to test whether the inclusion of natural levels of UV-B radiation in mutation-accumulation (MA) experiments influences the rate and effects of mildly deleterious mutation in the plant Arabidopsis thaliana. Ten generations of MA proved insufficient to observe significant changes in means or among-line variances in experimental lines maintained either with or without supplemental UV-B radiation. Maximum-likelihood estimates of mutation rate for total flower number revealed a small but significant rate of mutation for MA lines propagated under supplemental UV-B exposure, but not for those in which supplemental UV-B was omitted. A fraction of the flower number mutations under UV-B (approximately 25-30%) are estimated to increase flower number. Results from the application of transposon display to plant materials obtained after MA, in both the presence and absence of supplemental UV-B, suggest that the average rate of transposition for the class I and II transposable elements (TEs) surveyed was no more than 10(-4). Overall, the estimates of mutation parameters are qualitatively similar to what has been observed in other MA experiments with this species in which supplemental UV-B levels have not been used. As well, it appears that naturally occurring levels of UV-B do not lead to detectable increases in levels of transposable element activity.