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

Abstract

We found a consistent 3-site periodicity of the χ 2 9 values for the heterogeneity of the distribution of the second base in relation to the fi rst base of dinucleotides separated by 0 (contiguous), 1, 2, 3 … 17 (K) nucleotide sites in Drosophila mtDNA. Triplets of χ 2 9 values were found where the fi rst was over 300 and the second and third ranged between 37 and 114 (previous studies). In this study, the periodicity was signifi cant until separation of 2011K, and a structure of deviations from randomness among dinucleotides was found. The most deviant dinucleotides were G-G, G-C and C-G for the fi rst, second and third element of the triplet, respectively. In these three cases there were more dinucleotides observed than expected. This inter-bases correlation and periodicity may be related to the tertiary structure of circular DNA, like that of prokaryotes and mitochondria, to protect and preserve it. The mtDNA with 19.517 bp was divided into four equal segments of 4.879 bp. The fourth sub-segment presented a very low proportion of G and C, the internucleotide interaction was weaker in this subsegment and no periodicity was found. The maintenance of this mtDNA structure and organization for millions of generations, in spite of a high recurrent mutation rate, does not support the notion of neutralism or near neutralism. The high level of internucleotide interaction and periodicity indicate that every nucleotide is co-adapted with the residual genome.

Foundational errors in the Neutral and Nearly-Neutral theories of evolution in relation to the Synthetic Theory: Is a new evolutionary paradigm necessary?

“…High non-random internucleotide interactions are then expected as they were found in Bernardi's isochors (Bernardi, 1993(Bernardi, , 2007) and Karlin's signatures (Karlin and Mrazek, 1997). We found strong interactions among the nucleotides of a dinucleotide when they were separated by 0 (consecutive), 1, 2 … K nucleotide sites (Valenzuela, 2009(Valenzuela, , 2010(Valenzuela, , 2011(Valenzuela, , 2012Valenzuela et al, 2010). Also we found a periodicity every 3 sites not related to protein coding functions, in prokaryote DNA and mtDNA but not in eukaryote DNA (we recently found periodicities in eukaryotes, Solar et al, 2012).…”

“…Mutation and genetic drift could transitorily construct some DNA segments with hermeneutical (meaning sense, Valenzuela, 2009Valenzuela, , 2011 value, but, they cannot maintain them. Drift cannot drive evolution.…”

“…Table 6 shows the analysis of a DNA segment of the archeae Methanobrevibacter smithii (Valenzuela, 2012;AN = CP000678, REGION: 249362-255559, 6198bp). The analysis of dinucleotides whose bases are separated by 37 sites is performed (Valenzuela, 2009(Valenzuela, , 2010(Valenzuela, , 2011(Valenzuela, , 2012. We measured evolutionary fi tness, positive, negative and neutral selection by comparing with the expected random proportion of dinucleotides calculated with the frequency of bases of this DNA segment.…”

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

“…Is this deviation restricted to 17 sites of separations? Our study showed that significant values were found up to 2000 and more sites of separation [10, 13]; thus these interactions cannot be produced by coding or non-coding functions or any structural restrictions (this DNA has less than 20,000 bp, most of it is coding DNA and both strands are coding strands. Large separations imply that the first base is in one coding segment and the second is in another coding segment).…”

“…Table 2 shows the analysis for the mtDNA of Drosophila melanogaster (taken and adapted from [8] and [10], see the figure of base distribution in [10]). We observe the enormous deviation from neutrality of the total set of dinucleotides from 0 to 17 sites of separation.…”