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To avoid potential bias of divergence times in the molecular tree due to species sampling, the scaling constant was determined by a least-squares fit to the fossil data in the period 85 50 mya.
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It is then possible that the Aberranta-Amphinomida clade is, in fact, one of subgroups of the monophyletic Aciculata [ 10, 11], misplaced in most molecular trees (due to their strong attraction towards the outgroups?).
These problems persist due, in part, to the challenge of placing lineages that are species-poor and divergent in molecular trees, and due to the difficulty of assessing homologies among organisms with very diverse or reduced morphologies.
For instance in long-branch attraction types of scenarios where gene trees can not be consistently estimated from molecular sequences, MP-EST may consistently estimate a wrong species tree due to the bias in the gene tree reconstruction.
"The only way to domesticate trees is through genetic engineering," said Richard Meilan, associate professor of molecular tree physiology at Purdue.
We obtained 296 trees and were unable to compute one tree due to high sequence divergence.
Mapping of the 13 characters on the molecular tree gave us 13 trees, each with relative probabilities for every character state for every node in the tree.
Our approach searches a special tree structure called family tree, in which each vertex corresponds to a molecular tree.
The molecular tree obtained was compared to the 16S rRNA tree.
In growing a family tree, BfsSimEnum adds an atom to a molecular tree by BFS order.
BfsSimEnum constructs a family tree in which each vertex denotes a molecular tree.
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