Abstract
Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the most diversified subfamily. In both branches, synonymous substitution rates were elevated, indicating higher mutation rates. On early branches, mutations were biased in favour of AT content, which is consistent with a role for ultraviolet light-induced mutation and habitat shift. In ancestors of Podostemoideae, DNA-repair genes were enriched in genes under positive selection, which may have responded to the meristem architectural changes.
Highlights
Introduction= 1, P < 0.001), indicating that the preferred model is H2; that is, an elevation of substitution rates occurred at each stem branch in the family Podostemaceae and the subfamily Podostemoideae
Outgroup Outgroup ForegroundPodostemaceae TRI = WED, PODPatameter estimatesPodostemaceae: 2.57 TRI + WED: 2.25 POD: 4.74 Log-likelihood AIC (−2l + 2 K)POD Podostemoideae, TRI Tristichoideae, WED Weddellinoideae high-quality annotation is publicly available
Likelihood ratio tests were significant for H1 − H0 (2Δl = 48,901, d.f. = 1, P < 0.001) and H2 − H1 (2Δl = 38,248, d.f. = 1, P < 0.001), indicating that the preferred model is H2; that is, an elevation of substitution rates occurred at each stem branch in the family Podostemaceae and the subfamily Podostemoideae
Summary
= 1, P < 0.001), indicating that the preferred model is H2; that is, an elevation of substitution rates occurred at each stem branch in the family Podostemaceae and the subfamily Podostemoideae. In the basal branches of the subfamilies Tristichoideae and Weddellinoideae, we found that 98.1% (1609 genes) had higher evolutionary rates than those in the branches of the outgroups (Fig. 3a), and 98.5% (1616 genes) had higher evolutionary rates in the Podostemoideae branches compared with the basal subfamilies (Fig. 3b) In both cases, the distribution of relative rates was approximately lognormal, and the peaks clearly deviated from 1 The relative substitution rates became elevated to similar levels in both nucleotides and amino acids (mean values: 2.43 vs. 2.16 in basal subfamilies, 2.28 vs. 2.36 in Podostemoideae)
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