Algae Containing Chlorophylls a + c are Paraphyletic: Molecular Evolutionary Analysis of the Chromophyta

Bhattacharya, Debashish; Medlin, Linda K.; Wainright, Patricia O.; Ariztia, Edgardo V.; Bibeau, Claude; Stickel, Shawn K.; Sogin, Mitchell L.

doi:10.2307/2410032

Cited by 64 publications

(62 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Section: Bacterial Megaclassificationmentioning

confidence: 99%

“…The fact that complete rRNA sequences later supported their monophyly does not alter the fact that the morphological evidence against the premature conclusion was unwisely discounted. Other cases where morphology pointed to monophyly, but was more controversial, but where it was claimed to have been disproved by rRNA are the phylum Mycetozoa (apparently contradicted by numerous trees) and the kingdoms Plantae (contradicted by Bhattacharya et al, 1990) and Chromista (contradicted by Bhattacharya et al, 1991 ;Bhattacharya & Medlin, 1995 ;Oliveira & Bhattacharya, 2000).Protein trees have clearly established the monophyly of Mycetozoa (Baldauf & Doolittle, 1997 ;Baldauf et al, 2000) and Plantae sensu Cavalier-Smith 1981(Moreira et al, 2000Baldauf et al, 2000). The recent evidence from the duplication and retargeting of glyceraldehyde-phosphate dehydrogenase (Fast et al, 2001) decisively shows chromalveolates (Chromista plus alveolates ; Cavalier-Smith, 1999, 2000a to be monophyletic (McFadden, 2000), making it highly probable that Chromista are also.…”

mentioning

confidence: 99%

See 1 more Smart Citation

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

418

590

View full text Add to dashboard Cite

Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms : Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translationarrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids ; flagellar shaft of glycoprotein, not flagellin ; DNA-binding protein 10b ; specially modified tRNA ; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles ; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of T. Cavalier-Smith quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution : the fact that, during major evolutionary transformations, some org...

show abstract

Section: Bacterial Megaclassificationmentioning

confidence: 99%

mentioning

confidence: 99%

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

418

590

View full text Add to dashboard Cite

show abstract

“…In addition to diatom sequences presented in Bhattacharya et al (1992), we have included sequence data for five more diatom species (Tabl e 2), which have been deposited in Genbank. The sequences were aligned using two methods.…”

Section: Molecular Character Analysismentioning

confidence: 99%

“…Recently, Bhattacharya et al (1992) have shown, using small subunit (ssu) rRNA sequence data, that the diatoms are correctly placed in a chromophyte/ oomycete lineage that excludes dinoflagellates and prymnesiophytes. We have employed this same technique to assess the relationships among diatoms and the relationship of the diatoms to other groups within the chromophyte/oomycete lineage.…”

Section: Introductionmentioning

confidence: 99%

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

Medlin

Williams

Sims

1993

European Journal of Phycology

View full text Add to dashboard Cite

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.

show abstract

“…The haptophytes and stramenopiles share characteristics such as tubular mitochondrial cristae, similar storage products, and fucoxanthin that suggest a specific relationship between these taxa (9). Stramenopiles include autotrophic and heterotrophic species that may differ enormously in their morphology and mode of life.…”

mentioning

confidence: 99%

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Martens

Vandepoele

Peer

2008

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which wholesequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.gene gain ͉ gene loss

show abstract

Algae Containing Chlorophylls a + c are Paraphyletic: Molecular Evolutionary Analysis of the Chromophyta

Cited by 64 publications

References 16 publications

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Contact Info

Product

Resources

About