Genome size evolution of the extant lycophytes and ferns

Abstract

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

Keywords: Chromosome numbers; Evolution; Ferns; Genome size; Habitat type; Whole-genome duplications.

Fig. 1

Phylogenetic distribution of 2C values, numbers of chromosomes (2n), base number of chromosomes (x), and ploidy levels of 96 genera of ferns and lycophytes. Data for each genus were averaged from among all sampled species and transformed into percentages by dividing the maximum value for the genus. Within Polypodiales, phylogenetic nomenclature (i.e., the eupolypods) follows Smith et al. (2006).

Fig. 2

Logarithmic regression analysis comparing 2C values and spore sizes based on a, polar length (P); b, equatorial width (E); c, P/E ratio; and d, spore area.

Fig. 3

Correlation analysis between 2C values and chromosomal traits using logarithmic regression analysis.

Fig. 4

Relationships between genome size (2C) and a: chromosome number (2n); b: base number of chromosome (x); and c: ploidy level.

Fig. 5

ANOVA and regression analysis comparing 2C values and habitat types..

Fig. 6

Ancestral character reconstruction of different habitat types using a phylogeny representing 96 genera of lycophytes and ferns. Different colors represent different habitat types. The tree topology with node age constraints was generated in Phylocom v.4.2 based on Lehtonen et al. (2017).

Fig. 7

Scatterplots showing the relationships between genome size (pg) per unit time (million years, Myr) and probability of habitat type change per Myr. Hypothesis one (H1), shifts in habitat type occur prior to a change in genome size; Hypothesis two (H2), genome size changes occur simultaneously with habitat type shifts; Hypothesis three (H3), habitat type shift occur after changes in genome size. All plots show Pearson's R, p, a trendline, and the 95% CI (gray) for the model.