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.
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.
YUAN DeJianZHU ZuoBinTAN XiaoHuaLIANG JieZENG ChenZHANG JieGenCHEN JunMA LongDOGAN AycaBROCKMANN GudrunGOLDMANN OliverMEDINA EvaRICE Amanda D.MOYER Richard W.MAN XianYI KeLI YanKeLU QingHUANG YiMinHUANG Shi
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.
HU TaoBoLONG MengPingYUAN DeJianZHU ZhuBingHUANG YiMinHUANG Shi
