Internucleotide correlations and nucleotide periodicity in Drosophila mtDNA: New evidence for panselective evolution

Abstract

Analysis for the homogeneity of the distribution of the second base of dinucleotides in relation to the first, whose bases are separated by 0, 1, 2,… 21 nucleotide sites, was performed with the VIH-1 genome (cDNA), the Drosophila mtDNA, the Drosophila Torso gene and the human β-globin gene. These four DNA segments showed highly significant heterogeneities of base distributions that cannot be accounted for by neutral or nearly neutral evolution or by the "neighbor influence" of nucleotides on mutation rates. High correlations are found in the bases of dinucleotides separated by 0, 1 and more number of sites. A periodicity of three consecutive significance values (measured by the χ 2 9 ) was found only in Drosophila mtDNA. This periodicity may be due to an unknown structure or organization of mtDNA. This non-random distribution of the two bases of dinucleotides widespread throughout these DNA segments is rather compatible with panselective evolution and generalized internucleotide co-adaptation.

Heterogeneous periodicity of drosophila mtDNA: new refutations of neutral and nearly neutral evolution

“…It is probably related to the tertiary structure needed to fold the RNA virus into its capsid. In a second study we found similar correlations until K= 21, in Drosophila melanogaster mtDNA, Gene Torso, and in human beta globin (βHb) gene (Valenzuela, 2010a). However, the significance of the interaction was observed until K = 309 in HIV-1 and until K = 609 in mtDNA (Valenzuela 2010b).…”

“…Our study seeks to know the sequence information for tertiary or quaternary DNA structures (in relation to non-DNA molecules). We seek to affi rm or refute neutral, nearly neutral or selective evolution (Valenzuela and Santos, 1996, Valenzuela, 1997, 2007, 2010aValenzuela et al, 2010). Unexpectedly, we found a very high correlation between both bases of a dinucleotide separated by 0, 1, 2 …K (K= 35) nucleotide sites in the whole genome of the HIV-1 virus, and in one env gene of this virus (Valenzuela, 2009).…”

“…Studies of evolution have assumed that most or all evolutionary processes are directly or indirectly related to protein synthesis and regulation (Nei, 2005;Valenzuela, 2009Valenzuela, , 2010aNei et al, 2010). The acquisition and maintenance of the genetic code (as a whole) have been accepted non-critically as an out-ofevolution process.…”

“…), number of bases, tandem repeat segments, isochores, signatures and several other properties of the hereditary material. For example, no systematic evolutionary studies have been performed on the acquisition and maintenance of isochores and signatures present in the biotic world for more than a thousand million years (Valenzuela, 2007(Valenzuela, , 2009(Valenzuela, , 2010a. Recurrent forward and backward point and chromosome mutations occurring equally (neutrally) at any nucleotide site destroy inexorably any chromosome or gene organization.…”

“…Moreover, a three nucleotide periodicity was found only in mtDNA among these strong non-random distributions which is not related to protein synthesis coding functions (Valenzuela, 2010a(Valenzuela, , 2010b. This periodicity was seen in the series of χ 2 9 values [9 degrees of freedom due to four rows (less one) for the fi rst and fourth columns (less one) for the second nucleotide of the dinucleotide] that measure the distance to randomness (neutrality).…”