Fig 1.
Maximum likelihood phylogram of Isoetes nuclear ribosomal internal transcribed spacer.
Branch lengths are proportional to the expected number of substitutions per site, with scale bar representing 0.05 substitutions per site. Branches in bold have bootstrap support values greater than 90. Species in bold represent data generated in this study; nuclear ribosomal internal transcribed spacers for other Isoetes are from those used in Larsén and Rydin [18].
Fig 2.
Maximum likelihood phylograms of concatenated chloroplast and nuclear markers.
Phylograms are shown for a) concatenated chloroplast markers and b) concatenated nuclear markers. Branch lengths are proportional to the number of expected substitutions per site, with scale bar representing a) 0.07 and b) 0.2 substitutions per site. All bootstraps support values are 100 with the exception of the branch separating Ananas comosus from the clade containing Ceratophylum demersum in b), which has a support value of 85.
Fig 3.
Effect of different smoothing factors on Isoetes crown date estimation in r8s.
Estimated crown dates for Isoetes produced by r8s for concatenated chloroplast (green) and nuclear (blue) datasets are shown for a range of smoothing factors. The best fitting smoothing factor, as identified by cross validation, is highlighted for each dataset by a filled circle.
Fig 4.
Rate assignment on crown and stem branches of Isoetes in r8s.
The ratio of effective vs. assigned rates is shown for different smoothing factors in r8s for the stem branch of Isoetes (solid lines) and for the Isoetes crown branches (average; dashed lines), for the concatenated chloroplast (green) and nuclear (blue) datasets. Solid black line represents effective/assigned rate ratio of 1, for reference.
Table 1.
Estimates of Isoetes crown date.
Fig 5.
Quantile-quantile plot of BEAST rates for concatenated chloroplast markers.
The quantile-quantile plot of log10 transformed branch rates is shown for the concatenated chloroplast dataset in BEAST. The values for the Isoetes stem branch (blue) and crown branches (red) are highlighted.
Fig 6.
r8s versus BEAST Isoetes crown estimates for individual nuclear genes.
The scatterplot shows the estimates of the Isoetes crown date in r8s and BEAST for each individual nuclear gene. Line represents output of linear model using lm() function in R v3.5.2.
Fig 7.
Maximum clade credibility tree for combined nuclear subsamples in BEAST.
Node labels represent ages (Ma), blue bars represent 95% mean HPD intervals.