Progressive cross- and self-sterility associated with aging in fern clones and perhaps other plants

A somatic genetic clock for clonal species

Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species.

Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico

Background

Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity.

Methods

We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a greenhouse. We compared the genomic diversity, levels of inbreeding, genetic differentiation, and connectivity among studied sites and between adults and juvenile plants.

Results

Agave tequilana presented a genomic diversity of H_T = 0.12. The observed heterozygosity was higher than the expected heterozygosity. Adults were more heterozygous than juveniles. This could be a consequence of heterosis or hybrid vigor. We found a shallow genetic structure (average paired F_ST = 0.0044). In the analysis of recent gene flow, we estimated an average migration rate among the different populations of m = 0.25. In particular, we found a population that was the primary source of gene flow and had greater genomic diversity (H_E and H_O ), so we propose that this population should continue to be monitored as a potential genetic reservoir.

Discussion

Our results may be the consequence of more traditional management in the studied specific region of Jalisco. Also, the exchange of seeds or propagules by producers and the existence of gene flow due to occasional sexual reproduction may play an important role in maintaining diversity in A. tequilana. For populations to resist pests, to continue evolving and reduce their risk of extinction under a climate change scenario, it is necessary to maintain genetic diversity. Under this premise we encourage to continue acting in conservation programs for this species and its pollinators.

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.

On the ecological significance of pollen color: a case study in American trout lily (Erythronium americanum)

Evolutionary ecologists seek to explain the processes that maintain variation within populations. In plants, petal color variation can affect pollinator visitation, environmental tolerance, and herbivore deterrence. Variation in sexual organs may similarly affect plant performance. Within-population variation in pollen color, as occurs in the eastern North American spring ephemeral Erythronium americanum, provides an excellent opportunity to investigate the maintenance of variation in this trait. Although the red/yellow pollen-color polymorphism of E. americanum is widely recognized, it has been poorly documented. Our goals were thus (1) to determine the geographic distribution of the color morphs and (2) to test the effects of pollen color on components of pollen performance. Data provided by citizen scientists indicated that populations range from monomorphic red, to polymorphic, to monomorphic yellow, but there was no detectable geographic pattern in morph distribution, suggesting morph occurrence cannot be explained by a broad-scale ecological cline. In field experiments, we found no effect of pollen color on the probability of predation by the pollen-feeding beetle Asclera ruficollis, on the ability of pollen to tolerate UV-B radiation, or on siring success (as measured by the fruit set of hand-pollinated flowers). Pollinators, however, exhibited site-specific pollen-color preferences, suggesting they may act as agents of selection on this trait, and, depending on the constancy of their preferences, could contribute to the maintenance of variation. Collectively, our results eliminate some hypothesized ecological effects of pollen color in E. americanum, and identify effects of pollen color on pollinator attraction as a promising direction for future investigation.

Useful insights from evolutionary biology for developing perennial grain crops

Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.

Ageing of trees: application of general ageing theories

The main questions posed in ageing theories are how ageing evolved and whether or not it is programmed. While these questions have not yet been clearly resolved, several groups of possible theories have been published on this topic. However, most of these theories do not consider plants, and the specific traits involved in their ageing mechanisms. The first trait covers clonality and sectoriality and the second concerns the lack of a differentiated germ line. The lack of a germ line prevents telomere shortening which can lead to the transfer of somatic mutations into sexual offspring, while sectoriality in trees causes isolation of potentially catastrophic events in one tree part, thus creating a population of more or less independent modules within one axis. The processes of population dynamics, including ageing, can act within the framework of an individual tree as well as in that of the population as a whole, although the processes involved differ and consequently result in different effects.

The consequences of rare sexual reproduction by means of selfing in an otherwise clonally reproducing species

Clonal reproduction of diploids leads to an increase in heterozygosity over time. A single round of selfing will then create new homozygotic genotypes. Given the same allele frequencies, heritable genetic variation is larger when there are more extreme, i.e. homozygotic genotypes. So after a long clonal expansion, one round of selfing increases heritable genetic variation, but any fully or partially recessive deleterious alleles simultaneously impose a fitness cost. Here we calculate that the cost of selfing in the yeast Saccharomyces is experienced only by a minority of zygotes. This allows a round of selfing to act as an evolutionary capacitor to unlock genetic variation previously found in a cryptic heterozygous form. We calculate the evolutionary consequences rather than the evolutionary causes of sex. We explore a range of parameter values describing sexual frequencies, focusing especially on the parameter values known for wild Saccharomyces. Our results are largely robust to many other parameter value choices, so long as meiosis is rare relative to the strength of selection on heterozygotes. Results may also be limited to organisms with a small number of genes. We therefore expect the same phenomenon in some other species with similar reproductive strategies.

Missing domesticated plant forms: can artificial selection fill the gap?

In the course of their evolution, the angiosperms have radiated into most known plant forms and life histories. Their adaptation to a recently created habitat, the crop field, produced a novel form: the plant that allocates an unprecedented 30-60% of its net productivity to sexual structures. Long-lived trees, shrubs and vines of this form evolved, as did annual herbs. Perennial herb forms with increased allocation to asexual reproduction evolved, but there are no examples of perennial herbs with high sexual effort. We suggest that sowing seed into annually tilled fields favored shorter-lived herbs because of trade-offs between first-year seed production and relative growth rate and/or persistence. By propagating cuttings, people quickly domesticated tuber crops and large woody plants. Perennial herbs were too small to be efficiently propagated by cuttings, and the association between longevity, allogamy and genetic load made rapid domestication by sexual cycles unlikely. Perennial grain crops do not exist because they could not have evolved under the original set of conditions; however, they can be deliberately developed today through artificial phenotypic and genotypic selection.

Aging in a long-lived clonal tree

From bacteria to multicellular animals, most organisms exhibit declines in survivorship or reproductive performance with increasing age ("senescence"). Evidence for senescence in clonal plants, however, is scant. During asexual growth, we expect that somatic mutations, which negatively impact sexual fitness, should accumulate and contribute to senescence, especially among long-lived clonal plants. We tested whether older clones of Populus tremuloides (trembling aspen) from natural stands in British Columbia exhibited significantly reduced reproductive performance. Coupling molecular-based estimates of clone age with male fertility data, we observed a significant decline in the average number of viable pollen grains per catkin per ramet with increasing clone age in trembling aspen. We found that mutations reduced relative male fertility in clonal aspen populations by about 5.8 x 10(-5) to 1.6 x 10(-3) per year, leading to an 8% reduction in the number of viable pollen grains, on average, among the clones studied. The probability that an aspen lineage ultimately goes extinct rises as its male sexual fitness declines, suggesting that even long-lived clonal organisms are vulnerable to senescence.

Pollination mode and life form strongly affect the relation between mating system and pollen to ovule ratios

Pollen to ovule (P : O) ratios have been hypothesized to correlate with the degree of outcrossing and thus with the mating system of a plant. Also, P : O ratios are likely to vary with respect to pollination mode (i.e. wind pollination or animal pollination). Furthermore, constraints on the evolution of mating systems depending on life form may affect P : O ratios. We compiled P : O ratios and outcrossing rates for 107 angiosperm species and analyzed the relation between these traits considering pollination mode, life form and phylogenetic relatedness among species. In general, P : O ratios correlated significantly with outcrossing rates. However, when taking additional factors into account, the relation became ambiguous. The correlation was significantly positive in wind-pollinated species, but only marginally so in animal-pollinated species. Wind-pollinated species had higher P : O ratios than animal-pollinated taxa. In woody perennials, outcrossing was the predominant mating system and outcrossing rates did not correlate with P : O ratios. The results were not altered by accounting for phylogenetic relatedness among species. The results indicate that P : O ratios vary more strongly with pollination mode and life form than with the mating system.

High selfing and high inbreeding depression in peripheral populations of Juncus atratus

The mating system of a plant is the prime determinant of its population genetic structure. However, mating system effects may be modified by postzygotic mechanisms like inbreeding depression. Furthermore, historical as well as contemporary ecological factors and population characteristics, like the location within the species range can contribute to genetic variability. Using microsatellite markers we assessed the population genetic structure of the wind-pollinated Juncus atratus in 16 populations from peripheral and nearly central areas of the distribution range and studied the mating system of the species. In three peripheral populations, outcrossing rates at seeds stage were low (mean t(m) = 5.6%), suggesting a highly autogamous mating system. Despite this fact, on adult stage both individual heterozygosity (mean H(O) = 0.48) and gene diversity (mean H(E) = 0.58) were high even in small populations. Inbreeding coefficients were consistently low among all populations (mean F(IS) = 0.15). Within the three peripheral populations indirect estimates of lifetime inbreeding depression were surprisingly high (delta(eq) = 0.96) and inbreeding depression could be shown to act mostly on early seedling establishment. Similar conditions of autogamy combined with high inbreeding depression are typical for plants with a large lifetime genomic mutation rate that cannot avoid selfing by geitonogamy. However, the results presented here are unexpected for small-statured, herbaceous plants. Substantial genetic differentiation among all populations was found (mean F(ST) = 0.24). An isolation-by-distance pattern was apparent on large scale but not on local scale suggesting that the overall pattern was largely influenced by historical factors, e.g. colonization, whereas locally genetic drift was of greater importance than gene flow. Peripheral populations exhibited lower genetic diversity and higher inbreeding coefficients when compared with subcentral populations.

Forest fragmentation effects on patch occupancy and population viability of herbaceous plant species

Habitat fragmentation is one of the major threats to species diversity. In this review, we discuss how the genetic and demographic structure of fragmented populations of herbaceous forest plant species is affected by increased genetic drift and inbreeding, reduced mate availability, altered interactions with pollinators, and changed environmental conditions through edge effects. Reported changes in population genetic and demographic structure of fragmented plant populations have, however, not resulted in large-scale extinction of forest plants. The main reason for this is very likely the long-term persistence of small and isolated forest plant populations due to prolonged clonal growth and long generation times. Consequently, the persistence of small forest plant populations in a changing landscape may have resulted in an extinction debt, that is, in a distribution of forest plant species reflecting the historical landscape configuration rather than the present one. In some cases, fragmentation appears to affect ecosystem integrity rather than short-term population viability due to the opposition of different fragmentation-induced ecological effects. We finally discuss extinction and colonization dynamics of forest plant species at the regional scale and suggest that the use of the metapopulation concept, both because of its heuristic power and conservation applications, may be fruitful.

Evolutionary vestigialization of sex in a clonal plant: selection versus neutral mutation in geographically peripheral populations

The loss of traits that no longer contribute to fitness is widespread; however, the causative evolutionary mechanisms are poorly understood. Vestigialization could proceed through the fixation of selectively neutral degenerative mutations via genetic drift. Alternatively, selection may facilitate vestigialization if trait loss results in enhanced fitness. We tested these hypotheses using Decodon verticillatus, a clonal plant in which sexual sterility has arisen repeatedly in populations across the northern geographical range limit. We compared growth and survival of replicated genotypes from 7 sexually fertile and 18 sterile populations, over 3 years in a common environment. Survival of sterile genotypes was 53% greater than for fertile genotypes, but there was no difference in biomass accumulation. Almost all mortality, and hence increased performance of sterile genotypes, occurred during simulated overwinter dormancy. These observations suggest that selection has facilitated the vestigialization of sex, and thus do not support the neutral mutation hypothesis. The selective mechanism probably involves the relaxation of a genetic trade-off between sexual reproduction and survival: alleles that increase vegetative performance at the expense of sexual fertility are selected in geographically peripheral populations where sexual reproduction is suppressed by adverse environmental conditions.

Ageing in plants

Ageing in green plants differs in some fundamental ways from the process in animals. The seasonal cycle and persistence of a plant is governed by a combination of the determinate or indeterminate status of meristems (growth centres) and the cell death and disposal strategies employed by plants to generate well-adapted anatomies and morphologies. The degree of perenniality depends on the balance between exploratory growth and the wave of tissue death that succeeds it, and extremes of longevity can arise by relatively minor changes in the quantitative relationship between growth and death. The senescence and elimination of organs and tissues are related to the internal reallocation of resources but are programmed phases in the integrated development of the whole plant and do not represent a kind of ageing by stress or starvation. Meristems of long-lived plants accumulate genetic damage but selection mechanisms exist within the organism to control genetic load, and even to exploit somatic mutations that confer adaptive benefits. It is concluded that most plants do not age in the strict gerontological sense and that extremely long-lived forms like trees and clonal creeping perennials are sustained by selection and correction at the level of semi-autonomous cell lineages.

A conflict between two evolutionary levels in trees

Due to the lack of germ line segregation in plants, it is possible to consider plant evolution (but not the evolution of most animals) as being composed of two evolutionary levels: 1. Intra-organism, in which the replicating unit is a part of the tree (e.g. a branch), reproduction is asexual, mutations are somatic, and selection operates only upon traits relevant to vegetative growth. 2. Inter-organism, in which the replicating unit is the whole tree, reproduction is sexual, and selection operates upon all the traits. In this work, a case of a conflict between these two levels is studied. The dynamics of a mutation, which is advantageous on the branch level but harmful for the whole tree, are discussed for a one-locus two-allele model. Several cases are considered: dominant, partially dominant, and haploid. Necessary and sufficient conditions for fixation of such a mutation are found. The model predicts that as the longevity of a tree species increases, the trees are expected to be more strongly shifted from their optimal growth-to-reproduction ratio towards growth, and resource allocation between branches and other tree parts is expected to be shifted in favor of the branches. Traditional approach, considering the second level only, is justified as a limit case for short longevity.

Early-acting inbreeding depression and reproductive success in the highbush blueberry, Vaccinium corymbosum L

Tetraploid Vaccinium corymbosum genotypes exhibit wide variability in seed set following self- and cross-pollinations. In this paper, a post-zygotic mechanism (seed abortion) under polygenic control is proposed as the basis for fertility differences in this species. A pollen chase experiment indicated that self-pollen tubes fertilize ovules, but are also 'outcompeted' by foreign male gametes in pollen mixtures. Matings among cultivars derived from a pedigree showed a linear decrease in seed number per fruit, and increase in seed abortion, with increasing relatedness among parents. Selfed (S1) progeny from self-fertile parents were largely self-sterile. At zygotic levels of inbreeding of F>0.3 there was little or no fertility, suggesting that an inbreeding threshold regulates reproductive success in V. corymbosum matings. Individuals below the threshold are facultative selfers, while those above it are obligate outcrossers. Inbreeding also caused a decrease in pollen viability, and reduced female fertility more rapidly than male fertility. These phenomena are discussed in terms of two models of genetic load: (1) mutational load - homozygosity for recessive embryolethal or sub-lethal mutations and (2) segregational load - loss of allelic interactions essential for embryonic vigor. Self-infertility in highbush blueberries is placed in the context of 'late-acting' self-incompatibility versus 'early-acting' inbreeding depression in angiosperms.