'Non-coding' DNA actually codes indivdual differences

New research has found that most of the individual differences, some even related to genetic illnesses such as lupus or schizophrenia, do not depends on the 0.25% variation in coding DNA (genes) but on the quite larger (1-4%) diversity in non-coding regions of the genome (sometimes called "junk DNA"), which nevertheless directly influence how key proteins, known as transcription factors, bind to the actual genes.

In the words of co-researcher Michael Snyder:

... the bulk of the differences among individuals are not found in the genes themselves, but in regions we know relatively little about. Now we see that these differences profoundly impact protein binding and gene expression.

More details at Science Daily.

Relevant research papers:
- Maya Kasowski et al., Variation in Transcription Factor Binding Among Humans. Science, 2010. Pay per view.
- Wei Zheng et al., Genetic analysis of variation in transcription factor binding in yeast. Nature, 2010. Pay per view.

Mutation rate is "less than half"

From Science Daily.

Jard C. Roach et al., Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science, 2010. Pay per view.

By comparing the parents' DNA sequences to those of their children, the researchers estimated with a high degree of certainty that each parent passes 30 mutations -- for a total of 60 -- to their offspring.

Scientists long had estimated that each parent passes 75 gene mutations to their children.

That means an effective mutation rate of just 2/5 the usual estimates.

How to get life from the primordial ooze

While the potential for the basic bricks of life to form was demonstrated early in the history of modern science, how could these organic molecules get together to become the long chains of RNA or DNA, and hence life, has remained a mystery.

The problem is that oligonucleotides react and don't bind together under normal conditions. However researchers from the Georgia Institute of Technology have found now that certain "midwife" molecules, known more technically as "intercalators" cause such binding, creating longer polymers, RNA or DNA, the kernel of life.

Hence one of the main problems of paleo-biology seems to have been solved.

Read more at Science Daily.

DNA in sediments: a system for accurate DNA dating?

While the emphasis of this news item is that mammoths seem to have survived in some areas further than the fossil record suggests, up to at least 10,500 years ago, the true interest of this research for me is that they seem to have developed a novel technique to find ancient DNA in sediments, potentially freeing science from having to rely only on fossils for that purpose. Also the method allows for accurate archaeological datation of such DNA remains.

This is potentially revolutionary in the field of historical genetics (and others):

Dirt DNA has lots of exciting potential to contribute to extinction debates in other parts of the world too, as well as a range of archaeological questions," said Willerslev, who also points out that the approach is not restricted to looking back at the past. "We can also use it to make a list of modern species living in any particular location," he said.

Source: Science Daily. While the research is said to be published at PNAS, I can't find it - so I guess it's not still in print.

Molecular clock, two to six times slower than thought

Don't you just love it when you can say "I knew that!", "I told you!"

I did not have the hard evidence to prove it but I have been all the time arguing that the human molecular clock estimates (even by the standard Zhivotovski's compensated system) must be much older than normally claimed, at least twice.

Now penguins come to confirm my suspicion.

DNA from dead penguins that has remained frozen in Antarctica extreme conditions has demonstrated that the usual molecular clock age estimates are underestimated by 200 to 600 per cent.

In other words, a biological specimen determined by traditional DNA testing to be 100,000 years old may actually be 200,000 to 600,000 years old...

Source: Science Daily.

Original report: S. Subramanian et al., High mitogenomic evolutionary rates and time dependency. Trends in Genetics, 2009 (paywall).
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Adaptative evolution does not alter neutral mutation rates

A new research paper appears to demonstrate that adaptative evolution happens along the lines of neutral stochastic evolution and is not accelerated.

Kryazhimskiy S, Tkacik G, Plotkin JB, The dynamics of adaptation on correlated fitness landscapes. PNAS 2009 (right now the PDF is freely available)

From the Press release:

A major conclusion of the work is that for some organisms, possibly including humans, continued evolution will not translate into ever-increasing fitness. Moreover, a population may accrue mutations at a constant rate –- a pattern long considered the hallmark of “neutral” or non-Darwinian evolution -– even when the mutations experience Darwinian selection.

(...)

According to the study, a population’s fitness and substitution trajectories —t he mutations acquired to achieve higher fitness — depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. (...)

Researchers demonstrated that linear substitution trajectories that signify a constant rate of accruing mutations, long considered the hallmark of neutral evolution, can arise even when mutations are strongly beneficial.

If confirmed, this research should lay to rest the hypothesis that dismiss the informative value of genetic phylogenies based on presumpt adaptative selection: adaptative or not, mutations accumulate on similar rates, depending mostly on other factors, like population size (greater or weaker drift, possibly leading to fixation).
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Neanderthal genes even less likely to be within us

Found at Genes and Demons, based on a New Scientist's article:

Vindija Neanderthal genome is half-way into full sequencing and, this is the important part, some speculations can already be discarded:

1. Neanderthals did not have the microcephalin gene
2. Neanderthals did not have the increased fertility variant of Icelanders
3. Neanderthals were lactose intolerant
   

The full genome will take some other two years or so to be finished but these advanced conclusions again support the model of no (or extremely low) introgression from our native european cousins. There is nothing yet to support Neanderthal admixture in any degree, though, of course the possibility will likely remain open even after full sequencing.

Clovis not first Americans

It was already quite in doubt but the the finding of human mitochondrial DNA in fossilized faeces of a cave in Oregon, dated to 14,000 years ago, seems to settle the issue definitively. It also suggests that the first Native Americans followed the coastal route as the inner one wasn't available yet.

The mtDNA seems to be associated to people of East and North Asia.

Additionally they found several organic manufactured items: threads, basketry, rope, hides... all extremely rare findings for such an old site.

More in:
- University of Oregon: Researchers, led by UO archaeologist, find pre-Clovis human DNA.
- BBC: Faeces hint at first Americans.
- Science Daily: Pre-Clovis Human DNA found in 14,300-years-old Feces In Oregon Cave is Oldest In New World.

We have broken the Clovis sound barrier

(lead researcher Dennis Jenkins)