Supertree and supermatrix methods have great potential in the quest to build the tree of life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap-weighted matrix elements performed most effectively in this case, generating trees with the greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Nonindependence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations, with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semistrict consensus, enumerating shared clades and compatible clades. The semistrict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate 2 composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods.

Published phylogeny reconstructions of the palm family (Arecaceae) are based on plastid DNA sequences or restriction fragment length polymorphisms (RF

Plastid DNA sequences evolve slowly in palms but show that the family is monophyletic and highly divergent relative to other major monocot clades. It is therefore difficult to place the root within the palms because faster evolving, length‐variable sequences cannot be aligned with outgroup monocots, and length‐conserved regions have been thought to give too few characters to resolve basal nodes. To solve this problem, we combined 94 ingroup and 24 outgroup sequences from the length‐conserved rbcL gene with ingroup and alignable outgroup sequences from noncoding rps16 intron and trnL‐trnF regions. The separate rps16 intron and trnL‐trnF region contained about the same number of variable sites (autapomorphies not included) as rbcL, but gave higher retention indices and more clades with bootstrap support. In general, the strict consensus tree based on combined rbcL, rps16 intron, and trnL‐trnF data showed more resolution towards the base of the palm family than previous hypotheses of relationships of the Arecaceae. An important result was the position of subfamily Calamoideae as sister to the rest of the palms, but this received <50% bootstrap support. Another result of systematic significance was the indication that subfamily Phytelephantoideae is related to two tribes from subfamily Ceroxyloideae, Cyclospatheae and Ceroxyleae.

Mapped cpDNA restriction site characters were analyzed cladistically and the resulting phylogenetic hypotheses were used to test monophyly and relationships of the infrageneric classification of Lathyrus (Fabaceae) proposed by Kupicha (1983, Notes from the Royal Botanic Garden Edinburgh 41: 209–244). The validity of previously proposed classification systems and questions presented by these classification schemes were explored. Two cpDNA regions, rpoC (rpoC1, its intron, part of rpoC2, and their intergenic spacer) and IR⁻⁻ (psbA, trnH‐GUG, part of ndhF, and their intergenic spacers), were analyzed for 42 Lathyrus and two Vicia species. PCR (polymerase chain reaction) amplified rpoC and IR⁻⁻ products digested with 31 and 27 restriction endonucleases, respectively, resulted in 109 potentially informative characters. The strict consensus tree suggests that several of Kupicha's sections may be combined in order to constitute clades. The widespread section Orobus and the South American section Notolathyrus should be combined. Section Lathyrus, characterized by a twisted style, should either include sections Orobon and Orobastrum or be redefined as three sections, one of which is characterized by a 100 base pair deletion in the IR⁻⁻ region. Finally, a weighted parsimony analysis positions sections Clymenum (excluding L. gloeospermus) and Nissolia, both with phyllodic leaves, as sister sections. The affiliation of Lathyrus gloeospermus (section Clymenum) remains problematic.