Inverse relationship between genetic diversity and epigenetic complexity

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It has long been assumed that most parts of a genome and most genetic variations or SNPs are non-functional with regard to reproductive fitness. However, the collective effects of SNPs have yet to be examined by experimental science. We here developed a novel approach to examine the relationship between traits and the total amount of SNPs in panels of genetic reference populations. We identified the minor alleles (MAs) in each panel and the MA content (MAC) that each inbred strain carried for a set of SNPs with genotypes determined in these panels. MAC was nearly linearly linked to quantitative variations in numerous traits in model organisms, including life span, tumor susceptibility, learning and memory, sensitivity to alcohol and anti-psychotic drugs, and two correlated traits poor reproductive fitness and strong immunity. These results suggest that the collective effects of SNPs are functional and do affect reproductive fitness. collective effects, complex traits, minor alleles, SNPs, recombinant inbred lines, minor allele content (MAC) Citation:

Section: Optimum Genetic Diversitysupporting

confidence: 59%

mentioning

confidence: 99%

Scoring the collective effects of SNPs: association of minor alleles with complex traits in model organisms

Yuan

Zhu

Tan

et al. 2014

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“…We were naturally very surprised to find the genetic equidistance phenomenon and quickly realized the absurdity of the molecular clock interpretation. After three years of extensive studies, we published the maximum genetic diversity (MGD) hypothesis in 2008 and reinterpreted all major evolutionary phenomena, including the genetic equidistance result [8,28]. We also discovered a new aspect of the equidistance result, the overlap or coincident substitution feature, which has never been explained by any theory [27].…”

Section: The Maximum Genetic Diversity Hypothesis and The Genetic Equmentioning

confidence: 99%

“…The MGD hypothesis explained nearly all major evolutionary phenomena, and here we focus on the genetic equidistance result [6,8,28]. Over long evolutionary time scales or for fast-evolving sequences, we define "maximum genetic equidistance" in terms of maximum distance: different species are equidistant to a species of lower or equal complexity, and such distances do not change with time ( Figure 2(A) and (B)).…”

Section: The Maximum Genetic Diversity Hypothesis and The Genetic Equmentioning

confidence: 99%

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later

Long

Yuan

et al. 2013

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In 1963, Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species. This finding, together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962, directly inspired the ad hoc molecular clock hypothesis. Unfortunately, however, many biologists have since mistakenly viewed the molecular clock as a genuine reality, which in turn inspired Kimura, King, and Jukes to propose the neutral theory of molecular evolution. Many years of studies have found numerous contradictions to the theory, and few today believe in a universal constant clock. What is being neglected, however, is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery. In recent years, we fortuitously rediscovered the equidistance result, which remains unknown to nearly all researchers. Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity, we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena. The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology. genetic equidistance, overlap feature, evolution, molecular clock, neutral theory, maximum genetic diversity hypothesis, microevolution, macroevolution Citation:Hu T B, Long M P, Yuan D J, et al. The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later. Sci China Life Sci, 2013Sci, , 56: 254 -261, doi: 10.1007 Among the most interesting phenomena in biology are reproduction, heredity, and evolution. Biological evolution includes both phenotypes and molecules, which are modeled by the theory of natural selection and the neutral theory, respectively. Together, the two make up the modern evolutionary theory (MET). The neutral theory was proposed by Kimura, Jukes, and King to explain the observation that molecules evolved at a steady, clock-like rate [1,2]. But is the molecular clock a genuine universal phenomenon?1 A brief history of the molecular clock hypothesis and the neutral theory: how the molecular clock replaced the genetic equidistance phenomenonGenetic distance is a measure of molecular differences between species and is represented by the percentage differ-

“…The Modern Evolution Theory (MET) combines Darwin's and Kimura's theory. The Maximum Genetic Diversity (MGD) hypothesis is an alternative model that more tightly unites genotypes and phenotypes by greatly reducing the extent of neutral sequences [13,14]. Genetic diversity, defined here as percent position difference in the aligned sequence of homologous proteins or DNA created by point mutations, has a loose, inverse correlation with epigenetic complexity, defined as the total number of cell types and epigenetic molecules.…”

mentioning

confidence: 99%

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Huang

2012

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Unbiased readings of fossils are well known to contradict some of the popular molecular groupings among primates, particularly with regard to great apes and tarsiers. The molecular methodologies today are however flawed as they are based on a mistaken theoretical interpretation of the genetic equidistance phenomenon that originally started the field. An improved molecular method the 'slow clock' was here developed based on the Maximum Genetic Diversity hypothesis, a more complete account of the unified changes in genotypes and phenotypes. The method makes use of only slow evolving sequences and requires no uncertain assumptions or mathematical corrections and hence is able to give definitive results. The findings indicate that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade ~17.6 million years ago. Also, tarsiers are genetically closer to lorises than simian primates are. Finally, the fossil times for the radiation of mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous were independently confirmed from molecular dating calibrated using the fossil split times of gorilla-orangutan, mouse-rat, and opossum-kangaroo. Therefore, the re-established primate phylogeny indicates a remarkable unity between molecules and fossils.