Relationships among seed plants inferred from highly conserved genes: Sorting conflicting phylogenetic signals among ancient lineages

Susana Magallón, Michael Sanderson

Research output: Contribution to journalArticle

96 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1991-2006
Number of pages16
JournalAmerican Journal of Botany
Volume89
Issue number12
StatePublished - Dec 1 2002
Externally publishedYes

Fingerprint

Spermatophytina
sorting
Seeds
phylogenetics
seed
gene
phylogeny
Pinaceae
Genes
genes
codons
Codon
Gymnosperms
Chloroplast Genes
Embryophyta
Angiosperms
embryophytes
parsimony analysis
gymnosperm
Sequence Analysis

Keywords

  • Angiosperms
  • Gnetales
  • Gymnosperms
  • Long-branch attraction
  • Maximum likelihood
  • PsaA
  • PsbB
  • Third codon positions

ASJC Scopus subject areas

  • Plant Science

Cite this

Relationships among seed plants inferred from highly conserved genes : Sorting conflicting phylogenetic signals among ancient lineages. / Magallón, Susana; Sanderson, Michael.

In: American Journal of Botany, Vol. 89, No. 12, 01.12.2002, p. 1991-2006.

Research output: Contribution to journalArticle

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