The Root of the Tree: Lateral Gene Transfer and the Nature of the Domains

Walsh, David A.; Boudreau, Mary Ellen Rose.; Bapteste, Éric; Doolittle, W. Ford

doi:10.1002/9780470750865.ch3

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“…The current classification of this group is based mainly on four taxonomic characters: 16S rRNA gene sequence, polar lipid composition, phenotypic features and DNA-DNA hybridization (Oren et al, 1997;Grant et al, 2001). The value of RNA polymerase subunit B9 (rpoB9) gene sequence analysis for the classification of members of the family Halobacteriaceae has also been reported (Walsh et al, 2004;Minegishi et al, 2010).…”

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confidence: 99%

Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

Shimane

Hatada

Minegishi

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

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Strain YSM-79T was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5–5.3 M NaCl (optimum 2.5–3.0 M), pH 5.0–8.8 (optimum pH 5.2–6.3) and 20–55 °C (optimum 40 °C). Mg2+ is required for growth, with maximum growth at 200–300 mM Mg2+. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79T was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB′ gene sequence of strain YSM-79T had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79T should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79T ( = JCM 16327T = CECT 7563T).

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mentioning

confidence: 99%

Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

Shimane

Hatada

Minegishi

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

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“…Traits most relevant to a practical and flexible phenetic or ecological classification have often been acquired by LGT, not through VD. This is obviously so for many pathogenic bacteria (Deurenberg et al 2007;Vilas-Boas et al 2007), but is also true of such seemingly ancient and stable groups as the cyanobacteria (Coleman et al 2006) or haloarchaea (Walsh et al 2006). Phenetic classifications will of course remain tree-like if we persist in using methods that produce trees, but an underlying tree-like evolutionary process is not needed to explain them.…”

Section: Phenetics Cladistics and The Refutation Of The Tol Hypothesismentioning

confidence: 99%

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them

Doolittle

2009

Phil. Trans. R. Soc. B

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Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.

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The Root of the Tree: Lateral Gene Transfer and the Nature of the Domains

Cited by 2 publications

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Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them

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