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Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages
Author(s) -
Magallón Susana,
Sanderson Michael J.
Publication year - 2002
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.89.12.1991
Subject(s) - biology , phylogenetic tree , clade , sister group , pinaceae , phylogenetics , maximum parsimony , botany , evolutionary biology , maximum likelihood , gene , genetics , pinus <genus> , statistics , mathematics
Phylogenetic studies based on different types and treatment of data provide substantially conflicting hypotheses of relationships among seed plants. We conducted phylogenetic analyses of sequences of two highly conserved chloroplast genes, psaA and psbB, for a comprehensive taxonomic sample of seed plants and land plants. Parsimony analyses of two different codon position partitions resulted in well‐supported, but significantly conflicting, phylogenetic trees. First and second codon positions place angiosperms and gymnosperms as sister clades and Gnetales as sister to Pinaceae. Third positions place Gnetales as sister to all other seed plants. Maximum likelihood trees for the two partitions are also in conflict. Relationships among the main seed plant clades according to first and second positions are similar to those found in parsimony analysis for the same data, but the third position maximum likelihood tree is substantially different from the corresponding parsimony tree, although it agrees partially with the first and second position trees in placing Gnetales as the sister group of Pinaceae. Our results document high rate heterogeneity among lineages, which, together with the greater average rate of substitution for third positions, may reduce phylogenetic signal due to long‐branch attraction in parsimony reconstructions. Whereas resolution of relationships among major seed plant clades remains pending, this study provides increased support for relationships within major seed plant clades.