We allow for a heterogeneous landscape, where grid cells may be differentiated by the number of trees, the expected number of infected trees, rates of infection growth, and costs of surveillance and control.
Step 3(Q = LG as the default): Estimate trees, rates, etc., using Q and the phylogenetic software PhyML [ 18].
Last, we explore the impact of whole-tree rate constancy by relaxing this assumption and allowing five partitions (ANA + Magnoliidae, Monocotyledoneae, basal eudicots, Superrosidae and Superasteridae, see definition in Methods) of the angiosperm tree to evolve at their own rates26.
Given a rooted tree, rate variation among lineages is modelled using either local (LC) or discrete (DC) clocks.
Thus, although the use of genetic distances to calculate evolutionary correlations is valid, if they are used directly or in conjunction with a Neighbor-Joining tree, evolutionary rate and tree topology are conflated.
Following Hurst et al. ([2007]), two growth curves were calculated and presented, average tree growth rate and rapid tree growth rate.
Fortunately, previous studies discovered that the estimated coefficients of Q remained nearly unchanged when near-optimal phylogenetic trees and rate parameters were used [[ 10], and references therein].
Annual tree mortality rate (a) and annual tree recruitment rate (b) in relation to the maximum flooding level of the study plots.
Quantile regression was used to summarise the relationship between tree growth rate (mm year−1) and tree size (DBH), consistent with Hurst et al. ([2007]).
Maximum likelihood phylogenetic tree inferred from 16 genes from 51 taxa of angiosperms used as a constraint tree for rate comparisons.
