綿野 泰行

Abstract Cycads represent an example of the success of evolutionary stasis. Despite their early origin, they survived multiple events of mass extinction and diversified in modern tropical ecosystems during the Cenozoic without major changes in their morphology. What factors have allowed their persistence and diversification despite their conservative nature? We reviewed documentation on the micro‐ and macro‐evolutionary processes involved in the diversification of the Neotropical genus Dioon. Dioon comprises 18 species from varied habitats in Mexico and Honduras, and serves as a model to understand the patterns of cycad diversification. Here, we synthesize evidence reached from different fields, especially biogeography, phylogenetics, population ecology, and speciation, to propose a mechanism that can explain the current patterns of biodiversity in Dioon. At the macroevolutionary scale, a Paleogene origin for Dioon is more likely than an alternative hypothesis of a Neogene origin. Dioon lineages have dispersed along with the expansion of tropical forests throughout main mountain chains. Subsequently, climate change, and particularly aridification, promoted the fragmentation of the tropical forests, allowing the main Dioon clades to evolve in isolation at distinct biogeographic regimes. At the microevolutionary scale, low seed dispersal capability, stochastic demographic processes, and niche conservatism restrict the lineages to isolate themselves at narrow habitats, promoting local adaptation in populations. Local adaptation seems to be a process achieved through many generations under stabilizing selection. Altogether, these processes shaped the diversification in Dioon. This review attempts to stimulate further research on cycads and other biological groups that have diversified despite their apparent evolutionary stasis.

Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern—Phegopteris decursivepinnata—and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F₁ hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F₁ hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F₁ hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F₁ hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.

Abstract Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than twofold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.