6
Phylogenetic Analyses of
Large Data Sets: Approaches
Using the Angiosperms
DOUGlAS E. SOLTIS AND PAMElA S. SOLTIS
Department of Botany, Washington State University, Pullman, WA 99164-4238, USA
Abstract
Phylogeny is central to the understanding of biodiversity and evolutionary processes. However, elucidating phylogenetic relationships in many groups has remained problematic due to their sheer size. The feasibility of phylogenetic analyses
of large data sets has been questioned on both theoretical and empirical grounds.
Some have suggested that large data sets be broken into a series of smaller problems for phylogenetic analysis. However, recent empirical studies and critical developments in methods of data analysis indicate that large data sets are tractable.
We have learned a great deal about the analysis of large data sets via the angiosperms,
for which three large molecular data sets have been constructed (plastid atpB and
rbeL and nuclear I8S rDNA). We discuss three approaches successfully applied in
our analyses of these large data sets. Parsimony analyses of separate and combined
data sets representing hundreds of taxa indicate that "bigger is better." That is, both
empirical and simulation studies demonstrate that two solutions to dilemmas posed
by large data sets is the addition of taxa as well as characters. Recent developments
in software also greatly facilitate the parsimony analysis of large data sets. Applications such as NONA and the RATCHET can retrieve shorter trees than found by
PAUP, and in much shorter run times. The recent development of "quick search"
methods such as the fast bootstrap and fast jackknife are also of great utility in the
analysis of large data sets. These methods are rapid and emphasize only those clades
with strong support. All three of these approaches have recently been applied to a
567-taxon data set for angiosperms based on atpB, rbeL, and I8S rDNA sequences
(a total of 4733 bp/taxon). Analyses ofthe combined three-gene data set have yielded
Key words. phylogeny, large data sets, angiosperms, parsimony jackknife, fast bootstrap
91
Phylogenetic Analyses of
Large Data Sets: Approaches
Using the Angiosperms
DOUGlAS E. SOLTIS AND PAMElA S. SOLTIS
Department of Botany, Washington State University, Pullman, WA 99164-4238, USA
Abstract
Phylogeny is central to the understanding of biodiversity and evolutionary processes. However, elucidating phylogenetic relationships in many groups has remained problematic due to their sheer size. The feasibility of phylogenetic analyses
of large data sets has been questioned on both theoretical and empirical grounds.
Some have suggested that large data sets be broken into a series of smaller problems for phylogenetic analysis. However, recent empirical studies and critical developments in methods of data analysis indicate that large data sets are tractable.
We have learned a great deal about the analysis of large data sets via the angiosperms,
for which three large molecular data sets have been constructed (plastid atpB and
rbeL and nuclear I8S rDNA). We discuss three approaches successfully applied in
our analyses of these large data sets. Parsimony analyses of separate and combined
data sets representing hundreds of taxa indicate that "bigger is better." That is, both
empirical and simulation studies demonstrate that two solutions to dilemmas posed
by large data sets is the addition of taxa as well as characters. Recent developments
in software also greatly facilitate the parsimony analysis of large data sets. Applications such as NONA and the RATCHET can retrieve shorter trees than found by
PAUP, and in much shorter run times. The recent development of "quick search"
methods such as the fast bootstrap and fast jackknife are also of great utility in the
analysis of large data sets. These methods are rapid and emphasize only those clades
with strong support. All three of these approaches have recently been applied to a
567-taxon data set for angiosperms based on atpB, rbeL, and I8S rDNA sequences
(a total of 4733 bp/taxon). Analyses ofthe combined three-gene data set have yielded
Key words. phylogeny, large data sets, angiosperms, parsimony jackknife, fast bootstrap
91