Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR.
Author: Jimmy's Girl, The Puzzle Bark Tree, Drifting, The Windmill.
As I lay under a tree, drifting in and out of sleep, my thoughts spun from Romania to Greece, from Austria to Denmark, from clogs to berets to cheap cigarettes.
As I lay under a tree, drifting in and out of sleep, my thoughts spun from Romania to Greece, from Austria to Denmark, from clogs to berets to cheap fags.
The resulting alignments and the combined data sets of mitochondrial, nuclear, and all markers were analyzed using random and consensus sectorial searches, tree drifting, and 100 rounds of tree fusing in TNT v1.1 [33].
The driven searches included the ratchet [ 123], tree drifting, tree fusion and sectorial search [ 124].
We also ran TNT [ 23], using a combination of sectorial search, tree drifting, and fusing (i.e., techniques within TNT that are effective for large-scale parsimony analysis).
Parsimony tree searches were conducted using TNT 1.0 [ 53], with 10 ratchet iterations, 10 cycles of tree drifting and three rounds of tree fusing for each of 200 random addition sequences, coding gaps as 5th character and using five random addition sequences that included ten ratchet iterations, and three rounds of tree fusing using default settings.
We ran SuperFine+MRP based upon PAUP* (using the same parsimony ratchet implementation as MRP PAUP*)) and TNT (using the same combination of sectorial search, tree drifting, and fusing as MRP TNT)), and refer to these two different versions by SuperFine+MRP PAUP*) and SuperFine+MRP TNT).
The three-population test uses signal from genetic drift, which can detect quite old admixture but must overcome a counteracting contribution from postadmixture and off-tree drift.
For example, Melanesians are only found to be admixed according to the ALDER test; the inability of the three-population test to identify them as admixed is likely due to long off-tree drift from the Papuan branch prior to admixture.
