Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae).

Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.

Phenotypic trait variation in the North American Tragopogon allopolyploid complex.

PREMISE: Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time, we compared phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids. METHODS: Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness. We analyzed trait differences between allopolyploids and their parental species, and between synthetic and natural allopolyploids. RESULTS: As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to nonexistent trait differences. CONCLUSIONS: In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization.

Karyotypic variation and pollen stainability in resynthesized allopolyploids Tragopogon miscellus and T. mirus.

PREMISE OF THE STUDY: Polyploidy has extensively shaped the evolution of plants, but the early stages of polyploidy are still poorly understood. The neoallopolyploid species Tragopogon mirus and T. miscellus are both characterized by widespread karyotypic variation, including frequent aneuploidy and intergenomic translocations. Our study illuminates the origins and early impacts of this variation by addressing two questions: How quickly does karyotypic variation accumulate in Tragopogon allopolyploids following whole-genome duplication (WGD), and how does the fertility of resynthesized Tragopogon allopolyploids evolve shortly after WGD? METHODS: We used genomic in situ hybridization and lactophenol-cotton blue staining to estimate the karyotypic variation and pollen stainability, respectively, of resynthesized T. mirus and T. miscellus during the first five generations after WGD. KEY RESULTS: Widespread karyotypic variation developed quickly in synthetics and resembled that of naturally occurring T. mirus and T. miscellus by generation S4 . Pollen stainability in resynthesized allopolyploids was consistently lower than that of natural T. mirus and T. miscellus, as well as their respective diploid progenitor species. Logistic regression showed that mean pollen stainability increased slightly over four generations in resynthesized T. mirus but remained at equivalent levels in T. miscellus. CONCLUSIONS: Our results clarify some of the changes that occur in T. mirus and T. miscellus immediately following their origin, most notably the rapid onset of karyotypic variation within these species immediately following WGD.

Polyploidy and mutation in Arabidopsis.

The effects of genetic mutations are influenced by genome structure. Polyploids have more gene or allele copies than diploids, which results in higher tolerance of recessive deleterious mutations. However, this benefit may differ between autopolyploids and allopolyploids and between neopolyploids and older polyploid lineages due to the effects of hybridization and diploidization, respectively. To isolate these effects, we measured the impacts of controlled mutagenesis on reproductive fitness traits in closely related Arabidopsis diploids (A. thaliana), autotetraploids (A. thaliana), and allotetraploids (A. suecica), including both synthetic and natural polyploid lines. Overall, mutagenesis had the largest negative impacts on seed production, while its impacts on germination and survival were negligible. As expected, these effects were much stronger in diploids than in polyploids. The differences between autopolyploids, allopolyploids, and polyploids of different ages were minor-cumulative reproductive fitness did not significantly differ between the treatment and control groups for any polyploid line type. These results suggest that hybridization and polyploid age have not impacted the genomic redundancy of Arabidopsis polyploids enough to significantly alter their aggregate response to mutation, although this effect may differ in older polyploid lineages or in allopolyploids with different levels of divergence between parental subgenomes.

Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model.

Polyploidy contributes massively to the taxonomic and genomic diversity of angiosperms, but certain aspects of polyploid evolution are still enigmatic. The establishment of a new polyploid lineage following whole-genome duplication (WGD) is a critical step for all polyploid species, but this process is difficult to identify and observe in nature. Mathematical models offer an opportunity to study this process by varying parameters related to the populations, habitats, and organisms involved in the polyploid establishment process. While several models of polyploid establishment have been published previously, very few incorporate spatial factors, including spatial relationships between organisms, habitat shape, or population density. This study presents a stochastic, spatial model of polyploid establishment that shows how factors such as habitat shape and dispersal type can influence the fixation and persistence of nascent polyploids and modulate the effects of other factors. This model predicts that narrow, constrained habitats such as roadsides and coastlines may enhance polyploid establishment, particularly in combination with frequent clonal reproduction, limited dispersal, and high population density. The similarity between this scenario and the growth of many invasive or colonizing species along disturbed, narrow habitats such as roadsides may offer a partial explanation of the prevalence of polyploidy among invasive species.

Increased heterosis in selfing populations of a perennial forb.

Quantifying the importance of random genetic drift in natural populations is central to understanding the potential limits to natural selection. One approach is to estimate the magnitude of heterosis, the increased fitness of progeny derived from crosses between populations relative to crosses within populations caused by the heterozygous masking of deleterious recessive or nearly recessive alleles that have been fixed by drift within populations. Self-fertilization is expected to reduce the effective population size by half relative to outcrossing, and population bottlenecks may be common during the transition to selfing. Therefore, chance fixation of deleterious alleles due to drift in selfing populations should increase heterosis between populations. Increased homozygosity due to fixation or loss of alleles should also decrease inbreeding depression within populations. Most populations of the perennial herb Arabidopsis lyrata ssp. lyrata are self-incompatible (SI), but several have evolved self-compatibility and are highly selfing. We quantified heterosis and inbreeding depression in two predominantly self-compatible (SC) and seven SI populations in a field common garden experiment within the species' native range and examined the correlation between these metrics to gauge the similarity in their genetic basis. We measured proportion germination in the lab, and survival and fecundity (flower and seed production) for 2 years in the field, and calculated estimates of cumulative fitness. We found 7.2-fold greater heterosis in SC compared with SI populations, despite substantial heterosis in SI populations (56 %). Inbreeding depression was >61 %, and not significantly different between SC and SI populations. There was no correlation between population estimates of heterosis and inbreeding depression, suggesting that they have somewhat different genetic bases. Combined with other sources of information, our results suggest a history of bottlenecks in all of these populations. The bottlenecks in SC populations may have been severe, but their strong inbreeding depression remains enigmatic.