Sunday, June 26, 2016

Species biology as major determinants of genetic diversity

I recently found a Nature paper: Comparative population genomics in animals uncovers the determinants of genetic diversity  reporting findings on determinants of genetic diversity, which is well anticipated by the MGD theory.

The authors said:"Our analysis reveals that polymorphism levels are well predicted by species biology, whereas historical and contingent factors are only minor determinants of the genetic diversity of a species."

So, as we have said all along since 2008, genetic diversity in most cases have nothing to do with effective population size or bottle necks. It is largely determined by species complexity, which is the most important aspect of species biology. 

It is really great and satisfying to see that others have independently come to our point of view, even though they have yet to fully acknowledge our series of papers published since 2008.


Monday, June 20, 2016

Genomics: Special issue on the comprehensive functionality of genomic DNA

Genomics special issue to dump the junk DNA notion to junk yards

#genomics #genetics Editorial: Special issue on the comprehensive functionality of ge...

From the editorial by Huang: “About 80% of the human genome are transcribed but how much of it is functional is under hot debate. As one would immediately know if one takes an honest look at all the facts, the junk DNA position really is just hot air: it is neither supported by facts nor by axioms or self-evident logical reasoning, and has already been falsified by the failure of the universal molecular clock hypothesis. In fact, the exact opposite of neutrality should now become the null hypothesis because it is free of factual contradictions and accounts for all known facts.”

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. 

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
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)

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

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.

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


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.