XIANG, (JENNY) QIUYUN1*, MICHAEL MOODY2, DOUGLAS E. SOLTIS3, and PAMELA S. SOLTIS4. 1Department of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612, USA; 2Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269-4236, USA; 3Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611-5826, USA; 4Florida Museum of Natural History and the Genetics Institute, University of Florida, Gainesville, FL 32611 USA. - Effects of outgroups and long branches - An experiment with RASA and data from Cornales.
RASA was used to assess the suitability of various combinations of
outgroups and to identify potential long branches in the matK
and rbcL sequence data of Cornales. Results indicated that
several potentially problematic taxa having long branches in
individual data sets may have obscured phylogenetic signal, but when
data sets were combined RASA no longer detected long branch problems.
Our analyses also showed that a taxon having a long branch on the tree
may not be identified as a “long-branched” taxon by RASA. The long
branches identified by RASA had little effect on the arrangement of
other taxa in the tree, but the placements of the long-branched taxa
themselves were often problematic. Removing the long-branched taxa
from analyses generally increased bootstrap support, often
substantially. Use of non-optimal outgroups (as identified by RASA)
decreased phylogenetic resolution in parsimony analyses and suggested
different relationships in maximum likelihood analyses, although
usually weakly supported clades (less than 50% support) were impacted.
tRASA provides a more conservative measurements for
phylogenetic signal than the PTP and skewness tests. The separate
matK and rbcL sequence data sets were measured as not
containing phylogenetic signal by RASA, but PTP and skewness tests
suggested the reverse. Nonetheless, the matK and rbcL
sequence data sets suggested relationships within Cornales largely
congruent with those suggested by the combined matK-rbcL
sequence data that contains significant phylogenetic signal as
measured by tRASA, PTP, and skewness tests. Our results do
not recommend using tRASA as a sole criterion to discard data or taxa
in phylogenetic analyses, but tRASA and the taxon variance ratio
obtained from RASA may be useful as a guide for improved phylogenetic
analyses.
Key words: Cornales, long-branches, molecular phylogeny, phylogenetic signal, RASA