title: Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae).
abstract: A portion of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase (gpd) was sequenced in 26 representatives of the paleotropical moss, Mitthyridium, and a group of 20 outgroup taxa to assess its utility for phylogenetic reconstruction compared with the better understood chloroplast markers, rps4 and trnL. Primers based on plant and fungal sequences were designed to amplify gpd in plants universally with the exclusion of fungal contaminants. The piece amplified spanned 4 introns and 3 of 9 exons, based on comparisons with complete sequence from Arabidopsis. Size variation in gpd ranged from 891 to 1007 bp, in part attributable to 6 indels of variable length found within the introns. Intron 6 contributed most of the length variation and contained a variable purine-repeat motif of possible use as a microsatellite. Phylogenetic analyses of the full gpd amplicon yielded well-resolved trees that were in nearly full accord with the trees derived from the cpDNA partitions for analyses of both the ingroup and ingroup + outgroup taxon sets. Pairwise nucleotide substitution rates of gpd were as much as 2.2 times higher than those in rps4 and 2.8 times higher than in trnL. Excision of the introns left suitable numbers of parsimony informative characters and demonstrated that the full gpd amplicon could be compartmentalized to provide resolution for both shallow and deep phylogenetic branches. Exons of gpd were found to behave in a clock-like fashion for the 26 ingroup taxa and select outgroups. In general, gpd was found to hold great promise not only for improving resolution of chloroplast-derived phylogenies, but also for phylogenetic reconstruction of recent, diversifying lineages.
authors.affiliation: Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, USA. dpwall@stanford.edu
authors.forename: Dennis P
authors.initials: DP
authors.lastname: Wall
mesh_terms: D001482:Base Composition; D019068:Bryopsida / Q000145:classification / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; C097421:rps4 protein, plant; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases