The root was placed between diversification with a lineage-through-time plot and different survival models, although sensitive to missing data, suggest a gradual decrease in the average diversification rate.
The nine North American species of Rooted phylogenetic trees are essential for inferring the sequence of evolutionary events.
As expected, the outgroup criterion performed best when the length of the branch leading to the outgroup was short (Wheeler, 1990).
Simulations suggest that molecular clock analyses can correctly identify the root of a tree even when the clock assumption is severely violated.
Clock-based rooting of phylogenies may be particularly useful when outgroup rooting is problematic.
Here, we explore the application of relaxed-clock-rooting to resolve a difficult problem, namely the root of the genus .
This problem likely has resulted from the effects of numerous extinctions and a possible shift in net diversification rate (speciation rate minus extinction rate) in the genus, which we therefore also address.
Using real and simulated datasets, Huelsenbeck et al.
(2002) compared outgroup rooting, molecular clock–based rooting, and nonreversible models of DNA substitution and found that the outgroup and molecular clock criteria correctly identified the root a large proportion of the time.For comparison, we used midpoint and outgroup rooting and dating methods that rely on rooted input trees, namely penalized likelihood, a Bayesian autocorrelated-rates model, and a strict clock.The chloroplast sequences used here reject a single global substitution rate, and the assumption of autocorrelated rates was also rejected.Under the most extreme conditions of rate heterogeneity, the clock criterion identified the correct root roughly four times more often than did random rooting.(Rooting via a nonreversible model of DNA substitution performed poorly under most circumstances.) These results suggest that the root of a phylogenetic tree can be identified with “clock rooting” even when the substitution process is not strictly clocklike.Because is such a large and widespread clade, inferring its diversification has implications for our understanding of the Tertiary vegetation history of the Northern Hemisphere (Wolfe and Tanai, 1987; Boulter et al., 1996; Manchester, 1999).