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Implication for origin of species

Posted by forsdyke on 08 Apr 2007 at 19:00 GMT

Genome composition (GC%) can be estimated for prokaryotes either from a small group of genes [1], or from a single gene [2]. In the latter case, the correlation coefficient (0.99) for the 1144 base ftsY gene is superior to that for 19 other widely distributed and highly conserved genes. Although not stated by Min and Hickey, we can assume from the present context that there were no other mitochondrial genes (or 648 base segments) that would have provided a higher correlation coefficient than that for the gene encoding a cytochrome oxidase subunit (0.94).
Despite many problems [3], “barcoding” can facilitate classification into species and perhaps identification of newly emerging “cryptic species” for which there are no phenotypic correlates [4]. The differences observed may relate not only to differences between species, but to differences that originate species.

Min and Hickey show (Fig. 2b) that the predominant barcoding difference is at third synonymous codon positions, which correlates with a global change in GC% likely to affect all genes through synonymous (non-aminoacid-changing) mutations. Such changes have been observed, both directly [5] and indirectly [6], to appear early in the speciation process [7].

1. Zavala A, Naya H, Romero H, Sabbia V, Piovani R, Musto M (2005) Genomic GC content prediction in prokaryotes from a sample of genes. Gene 357:137-143.

2. Fournier P-E, Suhre K, Fournous G, Raoult D (2006) Estimate of prokaryotic genomic DNA G + C content by sequencing universally conserved genes. Int J Sys Evol Mic 56:1025-1029.

3. Rubinoff D, Cameron S, Will K (2006) A genomic perspective on the shortcomings of mitochrondrial DNA for ‘barcoding’ identification. J Hered 97:581-594.

4. Herbert PDH, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLOS Biology 2:e312.

5. Bellgard M, Schibeci D, Trifonov E, Gojobori TJ (2001) Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J Mol Evol 53:465-468.

6. Forsdyke DR (2007) Positive Darwinian selection. Does the comparative method rule? J Biol Sys 15:95-108.

7. Forsdyke DR (2006) Evolutionary Bioinformatics. Springer, New York.