title: Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids.
abstract: Photosynthetic eukaryotes contain primary, secondary or tertiary plastids, depending on the source of the organelle (a cyanobacterium or a photosynthetic eukaryote). Plastid phylogeny is relatively well investigated, but molecular phylogenies have conflicted as a function of gene choice, taxon-representations, and analytical method. To better understand the influences of these variables, we performed analyses of a multi-gene data set based on 62 plastid-associated genes of 15 taxa representing the major plastid lineages. In an attempt to distinguish phylogenetic signal from non-phylogenetic patterns, we analyzed the data using a wide range of phylogenetic methods and examined the effect of covarion evolution and compositional bias. The data suggest that the chlorophyll c-containing plastids are monophyletic and acquired their plastids from the red algae after the emergence of the Cyanidiales. The relationships among chl c-containing plastids are particularly hard to resolve. This is the largest data set used for this purpose; the analyses show that cryptophyte plastids are sister to other chl c-containing plastids, and haptophyte and peridinin-containing dinoflagellate plastids are closely related.
authors: Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742-5815, USA. mvs@indiana.edu
authors: M Virginia
authors: MV
authors: Sanchez-Puerta
authors: Tsvetan R
authors: TR
authors: Bachvaroff
authors: Charles F
authors: CF
authors: Delwiche
mesh_terms: D002734:Chlorophyll / Q000235:genetics*; D016678:Genome / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D010788:Photosynthesis; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D011506:Proteins / Q000235:genetics; D014908:Triticum / Q000235:genetics*
chemical_list: D009711:Nucleotides; D011506:Proteins; D002734:Chlorophyll; C064041:chlorophyll c