Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: the Drosophila saltans and willistoni groups, a case study.

Abstract excerpt

Rooting is frequently the most precarious step in any phylogenetic analysis. Outgroups can become useless for rooting if they are too distantly related to the ingroup. Specifically, little attention has been paid to scenarios where outgroups have evolved different nucleotide frequencies from the ingroup. We investigate one empirical example that arose seeking to determine the phylogenetic relationship between the...

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