Ploidy variation and hybridization
Using flow cytometry to estimate genome size on a subset of our samples,
we identified extensive ploidy variation associated with the three
genetically differentiated groups. Within P. vaginatum , the
fine-textured ecotype had an average estimated genome size consistent
with diploidy (1.01, when 1.0 is designated as the size of the diploidP. vaginatum reference genome) (Table 1). In contrast, the
relative genome size estimates for coarse-textured samples were
consistent with a mix of diploids (1.04) and triploids (1.56). ForPaspalum distichum , samples had higher average relative genome
size estimates overall, consistent with predictions that this species is
predominantly hexaploid and pentaploid (Echarte, Clausen, & Sala,
1992). Unlike P. vaginatum samples, P. distichum genome
size estimates did not form obvious multiples of the P. vaginatumreference genome. Instead, the difference in genome size between
putative pentaploids and hexaploids (2.25 and 2.69, respectively)
suggests a P. distichum basal genome size that is
~11% smaller than P. vaginatum . When P.
distichum relative genome sizes were recalculated assuming a basal
genome size of 0.89 instead of 1.0 as the point of reference, the values
closely match numerical expectations for pentaploid and hexaploid
genomes (2.53 and 3.03, respectively) (Table 1). Together these results
suggest that P. vaginatum is composed primarily of diploid and
triploid genotypes, that P. distichum is largely composed
of pentaploid and hexaploid genotypes, and that the basal genome size of
the latter species is likely ~11% smaller than theP. vaginatum reference genome.
By using genome-wide heterozygosity calls from the SNP dataset (F-values
generated by plink) in conjunction with the flow cytometry results
above, we were able to estimate ploidy for all genotypes (see Gompert &
Mock, 2017). Specifically, individuals containing multiple subgenomes
(e.g. allopolyploids) are expected to show an increase in heterozygosity
with each additional subgenome. The highest genome-wide heterozygosity
values (corresponding to more negative F-values) occurred in P.
distichum and were consistent with a combination of allohexaploid and
allopentaploid genotypes (average F = -1.323 and -1.241 respectively)
(Table 1). Conversely, the fine-textured cluster of P. vaginatum(composed entirely of diploids) had the lowest genome-wide
heterozygosity calls (average F = 0.541). For the coarse-texturedP. vaginatum group, which flow cytometry data indicated to be a
combination of diploids and triploids, F-values were consistent with a
slight increase in heterozygosity in putative triploids relative to
diploids (average F = -0.520 and -0.279 respectively). Unexpectedly,
there was a large difference in F-value between diploid coarse- and
fine-textured accessions (-0.278 and 0.541); the greater heterozygosity
in the coarse-textured genotypes, despite a lack of difference in genome
size, is potentially consistent with hybridization in the origin of the
diploid coarse-textured ecotype. Collectively these findings support the
inference that P. vaginatum not only falls into two genetically
distinct subgroups according to ecotype, but that the coarse-textured
ecotype can be further subdivided by ploidy variation.