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

The flower does not open in the city: evolution of plant reproductive traits of Portulaca oleracea in urban populations

BACKGROUND AND AIMS

The impact of urbanization on plant evolution, particularly the evolution of reproductive traits, remains largely unknown. In this study, we aimed to investigate the consequences of urbanization on the reproductive traits of Portulaca oleracea in the Kantō region of Japan. Portulaca oleracea has a unique cleistogamous reproductive system, which consists of genetically determined chasmogamous (open, CH) and cleistogamous (closed, CL) plants.

METHODS

We collected seeds of P. oleracea from ten populations in rural areas and ten populations in urban areas. In a common garden experiment, we recorded the type of flowers (CH or CL), reproductive phenology and seed production.

KEY RESULTS

All individuals produced either CH or CL flowers, allowing us to classify them as either CH or CL plants. We observed a significant difference in the prevalence of CH and CL plants between rural and urban populations: the number of CH plants was generally low and was particularly low among urban individuals. Compared to CH plants, CL plants showed earlier phenology and produced heavier seeds, which is consistent with stress avoidance in response to heat and drought stress conditions in urban areas.

CONCLUSIONS

Our findings suggest that urbanization may drive an evolutionary change in the cleistogamous reproductive system of P. oleracea. CL plants with earlier phenology and larger seeds might be better adapted to urban environments, where they are subjected to harsh heat and drought stress.

Measuring the Efficiency of Purging by non-random Mating in Human Populations

Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.

Early-acting inbreeding depression can evolve as an inbreeding avoidance mechanism

Despite the potential for mechanical, developmental and/or chemical mechanisms to prevent self-fertilization, incidental self-fertilization is inevitable in many predominantly outcrossing species. In such cases, inbreeding can compromise individual fitness. Unquestionably, much of this inbreeding depression is maladaptive. However, we show that when reproductive compensation allows for the replacement of inviable embryos lost early in development, selection can favour deleterious recessive variants that induce 'self-sacrificial' death of inbred embryos. Our theoretical results provide numerous testable predictions which could challenge the assumption that inbreeding depression is always maladaptive. Our work is applicable any species that cannot fully avoid inbreeding, exhibits substantial inbreeding depression, and has the potential to compensate embryos lost early in development. In addition to its general applicability, our theory suggests that self-sacrificial variants might be responsible for the remarkably low realized selfing rates of gymnosperms with high primary selfing rates, as gymnosperms exhibit strong inbreeding depression, have effective reproductive compensation mechanisms, and cannot evolve chemical self-incompatibility.

Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity

In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.

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.

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.

Population Genetic Analysis of the Threatened Plant Leavenworthia exigua var. laciniata (Brassicaceae) Reveals Virtually No Genetic Diversity and a Unique Mating System

Leavenworthia (Brassicaceae) has served as a model group for investigating the evolution of mating systems in plants, yet several Leavenworthia species remain understudied. One such taxon is Leavenworthia exigua var. laciniata, one of three varieties of L. exigua, a winter-annual plant endemic to the central United States. Because L. exigua var. laciniata occupies a narrow geographic range and is experiencing major habitat loss, it was recently listed as threatened; however, little is known about its genetic diversity and implications for conservation. We conducted a range-wide population genetic study of L. exigua var. laciniata and L. exigua var. exigua to understand: (1) levels of genetic diversity within and among populations, (2) whether L. exigua var. laciniata is genetically distinct from L. exigua var. exigua, and (3) implications for conservation. L. exigua var. laciniata showed identical genotypes at all 16 microsatellite loci across most of its range, fixed heterozygosity at some loci, and significant heterozygote excesses, consistent with a lack of recombination associated with an asexual mating system, which has not been documented previously in Leavenworthia. Because L. exigua var. laciniata is an annual and the same genotype occurs across multiple populations, asexuality may be caused by apomixis, asexual reproduction via seed. In contrast, most populations of L. exigua var. exigua demonstrated population genetic patterns consistent with a self-compatible mating system. Because L. exigua var. laciniata is morphologically, geographically, and genetically distinct, it should be recognized as an evolutionarily significant unit for conservation. We recommend maintaining large population sizes to conserve evolutionary potential in L. exigua var. laciniata, as the likelihood that facultative sexual reproduction may occur may be greater in larger populations. Additional research in L. exigua var. laciniata is needed to confirm the occurrence of asexuality and apomixis, clarify its reproductive isolation from other taxa, and to understand whether it exhibits residual sexual reproduction, epigenetic variation, or phenotypic plasticity to help it persist in response to environmental variation. In the future, L. exigua var. laciniata may serve as an important model in which to investigate the conservation of threatened plant species with little genetic variation in a changing climate.

Why are deleterious mutations maintained in selfing populations? An analysis of the effects of early- and late-acting mutations by a two-locus two-allele model

Frequencies of deleterious mutations are higher than expected in many plants. Here, by developing a two-locus two-allele model, I examine the effects of differential timing of the expression of deleterious mutations (two-stage effects) on the maintenance of mutations. I assume early- and late-acting loci to distinguish whether maintenance of mutations in populations with high selfing rates is explained better by two-stage effects of single mutations, or by separate mutations in both early- and late-acting loci. I found that, when ovules are overproduced, the stable frequency of early-acting mutations is higher if mutations also occur in a late-acting locus than if a late-acting mutation is lacking. The stable frequency of late-acting mutations is higher if mutations also occur in an early-acting locus than if an early-acting mutation is lacking. Selective interference does not account for these results because analyses in which the number of loci subject to mutations is equalized are included. Overproduction of ovules has little effect on maintenance if either early- or late-acting mutations are lacking, whereas when ovules are not overproduced, the two-stage effect does not enhance the maintenance of mutations. Hence, mutations occurring in both loci coupled with overproduction of ovules enhances the maintenance of mutations in populations with high selfing rates. The detailed mechanisms underlying the two-stage effect were also analyzed.

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

Addressing Darwin's dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load?

Darwin spent years investigating the effects of self-fertilization, concluding that "nature abhors perpetual self-fertilization." Given that selection purges inbred populations of strongly deleterious mutations and drift fixes mild mutations, why does inbreeding depression (ID) persist in highly inbred taxa and why do no purely selfing taxa exist? Background selection, associations and interference among loci, and drift within small inbred populations all limit selection while often increasing fixation. These mechanisms help to explain why more inbred populations in most species consistently show more fixed load. This drift load is manifest in the considerable heterosis regularly observed in between-population crosses. Such heterosis results in subsequent high ID, suggesting a mechanism by which small populations could retain variation and inbreeding load. Multiple deleterious recessive mutations linked in repulsion generate pseudo-overdominance. Many tightly linked load loci could generate a balanced segregating load high enough to sustain ID over many generations. Such pseudo-overdominance blocks (or "PODs") are more likely to occur in regions of low recombination. They should also result in clear genetic signatures including genomic hotspots of heterozygosity; distinct haplotypes supporting alleles at intermediate frequency; and high linkage disequilibrium in and around POD regions. Simulation and empirical studies tend to support these predictions. Additional simulations and comparative genomic analyses should explore POD dynamics in greater detail to resolve whether PODs exist in sufficient strength and number to account for why ID and load persist within inbred lineages.

How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae)

Genome-wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of Tolpis succulenta (Asteraceae) on Graciosa island in the Azores. These two known extant populations of T. succulenta on Graciosa have recently evolved self-compatibility. Despite the expectation that selfing would occur at an appreciable rate (self-incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self-incompatible colonists of T. succulenta from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self-compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season.

Epistasis, inbreeding depression, and the evolution of self-fertilization

Inbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may also generate an advantage to selfers in terms of more efficient purging, while the effects of epistasis among those alleles on inbreeding depression and mating system evolution remain little explored. In this article, we use a general model of selection to disentangle the effects of different forms of epistasis (additive-by-additive, additive-by-dominance, and dominance-by-dominance) on inbreeding depression and on the strength of selection for selfing. Models with fixed epistasis across loci, and models of stabilizing selection acting on quantitative traits (generating distributions of epistasis) are considered as special cases. Besides its effects on inbreeding depression, epistasis may increase the purging advantage associated with selfing (when it is negative on average), while the variance in epistasis favors selfing through the generation of linkage disequilibria that increase mean fitness. Approximations for the strengths of these effects are derived, and compared with individual-based simulation results.