Saturday, January 30, 2016

Evolution, Still a Theory in Crisis

More than thirty years after his landmark book Evolution: A Theory in Crisis (1985), biologist Michael Denton revisits his earlier thesis about the inability of Darwinian evolution to explain the history of life. He argues that there remains “an irresistible consilience of evidence for rejecting Darwinian cumulative selection as the major driving force of evolution.” buy it here

The book briefly introduced our interpretation of the genetic (molecular) equidistance phenomenon, called by Denton in his 1985 book as "one of the most astonishing findings of modern science." (see figure)





Sunday, January 17, 2016

Base composition variations in species from simple to complex

Li X, Scanlon MJ, Yu J (2015) Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems. Nucleic Acids Res 43: 3614-3625.

This paper shows striking patterns of base compositions. One of these as shown in supplementary figure 1 is that simple species such as bacteria show the widest range of base composition variation whereas primates show the least. This is of course expected from the MGD hypothesis. I only noticed this after meeting with the senior author of the paper. 



Total distrust of DNA work by famed Indo-European authority

I am studying Indo-European and Tocharin origins these days and found the following talks very helpful.


Pay attention to the 2nd talk by Mallory, archaeologist and authority on Indo-European languages. He said at the very beginning of his talk that he has total distrust of genetic work on ancient DNAs. He gave an example at the discussion part that Hungarians 1000 years ago were genetically very different from Hungarians today, which is totally nonsensical. Only we can make him and other archaeologists and paleontologists happy.

http://www.ncbi.nlm.nih.gov/pubmed/17632797 

here is the work on Hungarian DNA that I believe he was talking about.

Am J Phys Anthropol. 2007 Nov;134(3):354-68.
Comparison of maternal lineage and biogeographic analyses of ancient and modern Hungarian populations.
Tömöry G1, Csányi B, Bogácsi-Szabó E, Kalmár T, Czibula A, Csosz A, Priskin K, Mende B, Langó P, Downes CS, Raskó I.
Author information
Abstract
The Hungarian language belongs to the Finno-Ugric branch of the Uralic family, but Hungarian speakers have been living in Central Europe for more than 1000 years, surrounded by speakers of unrelated Indo-European languages. In order to study the continuity in maternal lineage between ancient and modern Hungarian populations, polymorphisms in the HVSI and protein coding regions of mitochondrial DNA sequences of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Sekler samples from Transylvania were analyzed. The data were compared with sequences derived from 57 European and Asian populations, including Finno-Ugric populations, and statistical analyses were performed to investigate their genetic relationships. Only 2 of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups, but some Asian affinities, and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations. Modern Hungarian-speaking populations seem to be specifically European. Our findings demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations, and no genetic continuity is seen.


Thursday, November 26, 2015

Compatibility between mitochondrial and nuclear genomes correlates with the quantitative trait of lifespan in Caenorhabditis elegans.

We just published a new paper in Sci Rep.

Scientific Reports 5, Article number: 17303 (2015)
doi:10.1038/srep17303

Compatibility between mitochondrial and nuclear genomes correlates with the quantitative trait of lifespan in Caenorhabditis elegans.

Abstract
Mutations in mitochondrial genome have epistatic effects on organisms depending on the nuclear background, but a role for the compatibility of mitochondrial-nuclear genomes (mit-n) in the quantitative nature of a complex trait remains unexplored. We studied a panel of recombinant inbred advanced intercrossed lines (RIAILs) of C. elegans that were established from a cross between the N2 and HW strains. We determined the HW nuclear genome content and the mitochondrial type (HW or N2) of each RIAIL strain. We found that the degree of mit-n compatibility was correlated with the lifespans but not the foraging behaviors of RIAILs. Several known aging-associated QTLs individually showed no relationship with mitotypes but collectively a weak trend consistent with a role in mit-n compatibility. By association mapping, we identified 293 SNPs that showed linkage with lifespan and a relationship with mitotypes consistent with a role in mit-n compatibility. We further found an association between mit-n compatibility and several functional characteristics of mitochondria as well as the expressions of genes involved in the respiratory oxidation pathway. The results provide the first evidence implicating mit-n compatibility in the quantitative nature of a complex trait, and may be informative to certain evolutionary puzzles on hybrids.


Saturday, November 21, 2015

Collective effects of common SNPs in foraging decisions in Caenorhabditis elegans and an integrative method of identification of candidate genes

A new paper of ours just published, demonstrating the power of the MGD theory in solving great puzzles of contemporary biology.

http://www.nature.com/articles/srep16904




 2015 Nov 19;5:16904. doi: 10.1038/srep16904.


Abstract

Optimal foraging decision is a quantitative flexible behavior, which describes the time at which animals choose to abandon a depleting food supply. The total minor allele content (MAC) in an individual has been shown to correlate with quantitative variations in complex traits. We have studied the role of MAC in the decision to leave a food lawn in recombinant inbred advanced intercross lines (RIAILs) of Caenorhabditis elegans. We found a strong link between MAC and the food lawn leaving rates (Spearman r = 0.4, P = 0.005). We identified 28 genes of unknown functions whose expression levels correlated with both MAC and leaving rates. When examined by RNAi experiments, 8 of 10 tested among the 28 affected leaving rates, whereas only 2 of 9 did among genes that were only associated with leaving rates but not MAC (8/10 vs 2/9, P < 0.05). The results establish a link between MAC and the foraging behavior and identify 8 genes that may play a role in linking MAC with the quantitative nature of the trait. The method of correlations with both MAC and traits may find broad applications in high efficiency identification of target genes for other complex traits in model organisms and humans.


Thursday, October 22, 2015

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



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.


References:
1. Ohta T, Gillespie JH (1996) Development of Neutral and Nearly Neutral Theories. Theor Popul Biol 49: 128-142.
2. Leffler EM, Bullaughey K, Matute DR, Meyer WK, Segurel L, et al. (2012) Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 10: e1001388.
3. Aquadro CF (1992) Why is the genome variable? Insights from Drosophila. Trends Genet 8: 355-362.
4. Lewontin RC (1991) Twenty-five years ago in Genetics: electrophoresis in the development of evolutionary genetics: milestone or millstone? Genetics 128: 657-662.
5. Lewontin RC (1974) The genetic basis of evolutionary change. New York and London: Columbia University Press.
6. Yuan D, Zhu Z, Tan X, Liang J, Zeng C, et al. (2014) Scoring the collective effects of SNPs: association of minor alleles with complex traits in model organisms. Sci China Life Sci 57: 876-888.
7. Zhu Z, Man X, Xia M, Huang Y, Yuan D, et al. (2015) Collective effects of SNPs on transgenerational inheritance in Caenorhabditis elegans and budding yeast. Genomics 106: 23-29.
8. Zhu Z, Yuan D, Luo D, Lu X, Huang S (2015) Enrichment of Minor Alleles of Common SNPs and Improved Risk Prediction for Parkinson's Disease. PLoS ONE 10: e0133421.
9. Yuan D, Zhu Z, Tan X, Liang J, Zeng C, et al. (2012) Minor alleles of common SNPs quantitatively affect traits/diseases and are under both positive and negative selection. arXiv:12092911.
10. Zhu Z, Lu Q, Zeng F, Wang J, Huang S (2015) Compatibility between mitochondrial and nuclear genomes correlates wtih quantitative trait of lifespan in Caenorhabditis elegans. Sci Rep: in press.
11. Zhu Z, Lu Q, Wang J, Huang S (2015) Collective effects of common SNPs in foraging decisions in Caenorhabditis elegans and an integrative method of identification of candidate genes. Sci Rep: in press.
12. Huang S (2009) Inverse relationship between genetic diversity and epigenetic complexity. Preprint available at Nature Precedings <http://dx.doi.org/10.1038/npre.2009.1751.2>
13. Huang S (2008) Histone methylation and the initiation of cancer, Cancer Epigenetics; Tollefsbol T, editor. New York: CRC Press.

14. Huang S (2012) Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers. Sci China Life Sci 55: 709-725.