Five burrow-morphological parameters (density, opening diameter, depth, branching and total burrow volume per m2) were measured.
We showed that simulated and real root systems had similar root distributions in terms of radial distance, depth, branching angle and branching order.
In O. sativa, significant genetic variation has been observed in root number, diameter, depth, branching, vertical density distribution, root-to-shoot ratio, water extraction, and root penetration (O'Toole and Bland 1987; Lafitte et al. 2001).
The most common underground method of ore extraction is cut-and-fill stoping, in which tunnels are dug to moderate depths, branching away from the mine portals.
Because shorter branches were estimated more accurately than longer branches, when the depth 2 branch of the 4-taxon simulation tree was half the length of the four depth 1 branches, we expected the depth 2 branch to be less underestimated than the depth 1 branches in the tree.
However, for longer branches (≥0.7 substitutions/site), depth 2 branch length estimates were affected by the degree of misestimation of the "majority" branch length (1.4 substitutions/site); in these cases, when the depth 2 branch length was halved, its length was more overestimated than expected based on the 8-taxon depth 2 results.
Finally, we tested for a relationship between node depth and branch length (given the possibility that greater congruence on deeper branches might be explained by deeper branches being longer).
The percentage by which each depth 1 branch was underestimated was graphed as a function of true branch length using R [ 59].
When the depth 2 branch was double the length of the four depth 1 branches in the 4-taxon simulation tree, the depth 2 branch was more underestimated than the depth 1 branches in the tree, as predicted; however, the depth 2 branch was underestimated at a rate significantly lower than depth 2 branches of the same length for the 8-taxon equal-branch-length tree.
Doubling or halving the length of the depth 2 branch of a 4-taxon tree had no effect on depth 1 branch length estimation.
However, this half-length depth 2 branch was actually underestimated at a rate similar to the depth 1 branches of the 4-taxon tree, which was significantly higher than the rate of underestimation for depth 2 branches for the 8-taxon equal branch length tree.
