New thoughts on an old riddle: what determines genetic diversity within and between species?

We just published a preprint on arXiv "New thoughts on an old riddle: what determines genetic diversity within and between species?"

http://arxiv.org/abs/1510.05918 

The abstract and the introduction section of the paper are posted below.

Abstract

The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic diversity by using MET. We here examine the two key experimental observations of genetic diversity made in the 1960s, one between species and the other within a population of a species, that directly contributed to the development of MET. The interpretations of these observations as well as the assumptions by MET are widely known to be inadequate. We review the recent progress of an alternative framework, the maximum genetic diversity (MGD) hypothesis, that uses axioms and natural selection to explain the vast majority of genetic diversity as being at optimum equilibrium that is largely determined by organismal complexity. The MGD hypothesis fully absorbs the proven virtues of MET and considers its assumptions relevant only to a much more limited scope. This new synthesis has accounted for the much overlooked phenomenon of progression towards higher complexity, and more importantly, been instrumental in directing productive research into both evolutionary and biomedical problems.   

Introduction

The modern evolutionary theory (MET) consists of Darwin’s theory of natural selection and Kimura’s Neutral theory (also Ohta’s Nearly Neutral theory). The theory treats evolution the same as population genetics. The Darwinian theory is much better known than the Neutral theory. However, for molecular evolution and population genetics, the Neutral theory (and the Nearly Neutral theory) has been more useful. Regardless, however, the MET is still incomplete, as acknowledged by Ohta and Gillespie: "..we have yet to find a mechanistic theory of molecular evolution that can readily account for all of the phenomenology. ..we would like to call attention to a looming crisis as theoretical investigations lag behind the phenomenology." [1].

Key puzzles of evolution remain unsolved by the MET. The central problem of the field is and has always been the old riddle of what determines genetic diversity [2-5]. Is it mostly determined by natural selection or neutral drift? Here we critically examine the historical origins and assumptions of the MET. We show that both the neutral and the selection frameworks were largely mistaken right from the beginning. Key observations that directly inspired the neutral theory were nearly half of a century ahead of their time. Selection schemes on the other hand was largely influenced by the one gene one trait genetics of the early 1900s and always treated single locus as the target of selection, which is in fact rarely the case for most of the commonly observed variations as recent studies have shown [6-11]. Finally, we review a candidate for superseding the MET, the maximum genetic diversity (MGD) hypothesis first published in 2008 [12,13], that fully absorbs the proven virtues of the MET and has more explanatory power as well as greater value in directing productive research in a much wider field of biomedical science [6-11,14]. The old riddle of genetic diversity within and between species is solved as mere deductions of the assumptions of the MGD. Only in this case, the assumptions are, for the first time in biology, self-evident intuitions that are no less true or false than any known axioms of hard sciences or mathematics.

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