Phylogeny of Dinoflagellate Plastid Genes Recently Transferred to the Nucleus Supports a Common Ancestry with Red Algal Plastid Genes

[1]  N. Patron,et al.  Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra. , 2006, International journal of systematic and evolutionary microbiology.

[2]  N. Patron,et al.  A tertiary plastid uses genes from two endosymbionts. , 2006, Journal of molecular biology.

[3]  H. Brinkmann,et al.  A “Green” Phosphoribulokinase in Complex Algae with Red Plastids: Evidence for a Single Secondary Endosymbiosis Leading to Haptophytes, Cryptophytes, Heterokonts, and Dinoflagellates , 2006, Journal of Molecular Evolution.

[4]  D. Morse,et al.  Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium , 2006, Nucleic acids research.

[5]  C. Delwiche,et al.  Rate Variation as a Function of Gene Origin in Plastid-Derived Genes of Peridinin-Containing Dinoflagellates , 2006, Journal of Molecular Evolution.

[6]  C. Delwiche,et al.  Chlorophyll c-containing plastid relationships based on analyses of a multigene data set with all four chromalveolate lineages. , 2005, Molecular biology and evolution.

[7]  Naiara Rodríguez-Ezpeleta,et al.  Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes , 2005, Current Biology.

[8]  N. Patron,et al.  Complex protein targeting to dinoflagellate plastids. , 2005, Journal of molecular biology.

[9]  D. Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[10]  D. Bhattacharya,et al.  Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. , 2005, Molecular biology and evolution.

[11]  F. Delsuc,et al.  Phylogenomics and the reconstruction of the tree of life , 2005, Nature Reviews Genetics.

[12]  P. Keeling,et al.  HSP90, Tubulin and Actin are Retained in the Tertiary Endosymbiont Genome of Kryptoperidinium foliaceum , 2004, The Journal of eukaryotic microbiology.

[13]  A. Barbrook,et al.  Dinoflagellate chloroplasts--where have all the genes gone? , 2004, Trends in genetics : TIG.

[14]  V. Lilakoumandou.  Dinoflagellate chloroplasts ? where have all the genes gone? , 2004 .

[15]  C. Delwiche,et al.  Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. , 2004, Protist.

[16]  M. Soares,et al.  Migration of the Plastid Genome to the Nucleus in a Peridinin Dinoflagellate , 2004, Current Biology.

[17]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[18]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[19]  D. Morse,et al.  Plastid ultrastructure defines the protein import pathway in dinoflagellates , 2003, Journal of Cell Science.

[20]  G. McFadden,et al.  Comment on "A Green Algal Apicoplast Ancestor" , 2003, Science.

[21]  P. Keeling,et al.  64 Nucleus‐encoded, plastid‐targeted glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids , 2003 .

[22]  Lucie Maranda,et al.  PHYLOGENETIC EVIDENCE FOR THE CRYPTOPHYTE ORIGIN OF THE PLASTID OF DINOPHYSIS (DINOPHYSIALES, DINOPHYCEAE) 1 , 2003 .

[23]  J. Palmer,et al.  THE SYMBIOTIC BIRTH AND SPREAD OF PLASTIDS: HOW MANY TIMES AND WHODUNIT? , 2003 .

[24]  Christopher J. Tonkin,et al.  Dissecting Apicoplast Targeting in the Malaria Parasite Plasmodium falciparum , 2003, Science.

[25]  M. King,et al.  A Green Algal Apicoplast Ancestor , 2002, Science.

[26]  D. Bhattacharya,et al.  From the Cover: The single, ancient origin of chromist plastids , 2002 .

[27]  B. Green,et al.  Second- and third-hand chloroplasts in dinoflagellates: Phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. Keeling,et al.  Re-examining Alveolate Evolution Using Multiple Protein Molecular Phylogenies , 2002, The Journal of eukaryotic microbiology.

[29]  T. Cavalier-smith,et al.  Dinoflagellate Nuclear SSU rRNA Phylogeny Suggests Multiple Plastid Losses and Replacements , 2001, Journal of Molecular Evolution.

[30]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[31]  D. Roos,et al.  Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. , 2001, Molecular biology and evolution.

[32]  W. Doolittle,et al.  A kingdom-level phylogeny of eukaryotes based on combined protein data. , 2000, Science.

[33]  C. Delwiche,et al.  Phylogenetic analyses indicate that the 19'Hexanoyloxy-fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin. , 2000, Molecular biology and evolution.

[34]  Charles F. Delwiche,et al.  Tracing the Thread of Plastid Diversity through the Tapestry of Life , 1999, The American Naturalist.

[35]  Hidetoshi Shimodaira,et al.  Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.

[36]  T. Cavalier-smith,et al.  Single gene circles in dinoflagellate chloroplast genomes , 1999, Nature.

[37]  D. Morse,et al.  The Phylogeny of Glyceraldehyde-3-Phosphate Dehydrogenase Indicates Lateral Gene Transfer from Cryptomonads to Dinoflagellates , 1998, Journal of Molecular Evolution.

[38]  M. Hasegawa,et al.  Gene transfer to the nucleus and the evolution of chloroplasts , 1998, Nature.

[39]  Yves Van de Peer,et al.  Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA , 1997, Journal of Molecular Evolution.

[40]  L. Medlin,et al.  Ribosomal RNA Analysis Indicates a Benthic Pennate Diatom Ancestry for the Endosymbionts of the Dinoflagellates Peridinium foliaceum and Peridinium balticum (Pyrrhophyta) , 1997, The Journal of eukaryotic microbiology.

[41]  J. Palmer,et al.  A Plastid of Probable Green Algal Origin in Apicomplexan Parasites , 1997, Science.

[42]  J. Palmer,et al.  Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. , 1996, Molecular biology and evolution.

[43]  Geoffrey I. McFadden,et al.  Plastid in human parasites , 1996, Nature.

[44]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[45]  H. Kishino,et al.  Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea , 1989, Journal of Molecular Evolution.

[46]  M. Chihara,et al.  A GREEN DINOFLAGELLATE WITH CHLOROPHYLLS a and b: MORPHOLOGY, FINE STRUCTURE OF THE CHLOROPLAST AND CHLOROPHYLL COMPOSITION 1 , 1987 .

[47]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[48]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[49]  G. McFadden,et al.  The apicoplast: a review of the derived plastid of apicomplexan parasites. , 2005, Current issues in molecular biology.

[50]  P. Keeling,et al.  On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. , 2005, International journal of systematic and evolutionary microbiology.

[51]  G. McFadden,et al.  A Phylogenetic Assessment of the Eukaryotic Light-Harvesting Antenna Proteins, with Implications for Plastid Evolution , 1999, Journal of Molecular Evolution.

[52]  J. Wolters,et al.  The troublesome parasites--molecular and morphological evidence that Apicomplexa belong to the dinoflagellate-ciliate clade. , 1991, Bio Systems.