we have used MrBayes software on about 400 full length 18S rDNA (1700 bp)with the TGR model of evolution. With MrBayes, the bootstrap support for deeper (and basically all) phylogenetic nodes is strikingly high (about 100%). Does anybody have the same experience with MrBayes ? Does anybody know some relevant literature on this ? (Our NJ trees with PAUP have remarkably low support at deeper nodes).
Thanks in advance for any help,
Andre van der Wurff