Oldest DNA sequences may reveal secrets of ancient animal ancestors

October 28, 2015, University of Leicester

700 million year-old DNA sequences from ancient animals have been unearthed by researchers at the Universities of Leicester and Warwick, shedding new light on our earliest animal ancestors and how they influenced modern species – including the sponge.

The team, led by Dr Eran Tauber (Leicester) and Dr Sascha Ott (Warwick) has discovered highly conserved sequences in non-coding DNA by analysing the genome sequences of 12 different insects – and have identified a set of 322 non-coding DNA regions which have been evolutionarily preserved for at least 180 million years.

The ancient sequences were found to be present in a wide variety of modern animals including insects, mammals, reptiles, jellyfish, and even our most distant animal ancestor, the sponge.

The youngest sequences uncovered by the analysis are conserved among bees, ants, and wasps (the Hymenoptera), while the two oldest sequences have been conserved for at least 670 million years – making them among the oldest regulatory DNA sequences of which we know, and would have been present in some of our earliest animal ancestors.

The oldest sequence uncovered by the analysis has been shown to be involved in control of translation in the early embryo, ensuring that the right genes are switched on and off for this crucial stage of development.

Dr Tauber of the Department of Genetics at the University of Leicester said: "We are extremely excited about identifying these ancient DNA elements. Their conservation indicates that they serve an important function, and there is already some experimental evidence to suggest that this is indeed the case.

"We are looking forward now to uncovering the specific function of these DNA elements using molecular biology and genetic engineering in our laboratory."

Only a small part of the genome consists of genes - stretches of DNA sequences that are translated into proteins. These sequences evolve slowly and are generally well conserved between different organisms.

Dr Tauber explained: "The slow evolution of proteins means that, when a new species is sequenced, protein-coding sequences can be easily detected by computationally comparing the sequences of known proteins with the newly sequenced genome.

"The majority of the genome, however, consists of DNA which does not code for proteins. These sequences generally evolve faster than protein-coding sequences, and so identifying functional elements within these sequences is more challenging."

All of the ancient conserved elements dating from more than 180 million years ago are part of the upstream untranslated regions of transcripts, and occur in a number of key translational regulatory genes.

Some of these sequences have been studied previously, and have been shown to be involved in the regulation of protein translation.

Dr Sascha Ott, Associate Professor in Systems Biology at the University of Warwick, said: "Our comprehensive approach allows us to pinpoint genes such as the Osiris gene cluster which has six deeply conserved regions and is vastly under-studied in comparison to other gene clusters with such a rare make-up.

"As insects are likely to become an increasingly significant part of food security strategies the understanding of insect-specific regulatory systems such as the Osiris genes is relevant."

Nathaniel Davies, a PhD student and first author of the paper from the Tauber lab at the University of Leicester said: "This study adds to our knowledge of the known sequences, showing that these sequences have been doing their job for a very long time, and provides scientists with a collection of interesting new to investigate."

Explore further: Human 'junk' gene sequences can promote translation

More information: Nathaniel J. Davies et al. Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals, BMC Evolutionary Biology (2015). DOI: 10.1186/s12862-015-0499-6

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JVK
1 / 5 (4) Oct 29, 2015
http://www.biomed...8/15/227
"...we use the emerging model organism Nasonia vitripennis..."

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
Excerpt: In wasps, manipulation of the genetics of evolved species-specific pheromones characterized the change in a pre-existing signaling molecule triggered by a glucose-dependent (Yadav, Joshi, & Gurjar, 1987) stereochemical inversion (Niehuis et al., 2013).

Niehuis O, Buellesbach J, Gibson J. D, Pothmann D, Hanner C, Mutti N. S, et al. Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones. Nature. 2013;494:345–348.

Anyone who uses a model organism I used to exemplify what is known to serious scientists about biologically-based cause and effect should not try to use the same model organism to support their ridiculous claims about millions of years of evolution.
Vietvet
5 / 5 (3) Oct 29, 2015

Anyone who uses a model organism I used to exemplify what is known to serious scientists about biologically-based cause and effect should not try to use the same model organism to support their ridiculous claims about millions of years of evolution.


@JVK

You certainly are not a "serious scientists", you are a young earth creationist crank. And your "model" is fatally flawed.
"Criticisms of the nutrient-dependent pheromone-controlled evolutionary model"
http://www.ncbi.n...4049134/
JVK
1 / 5 (4) Oct 29, 2015
The Nasonia vitripennis model organism exemplifies the fact that nutrient-dependent microRNAs control expression of genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans. That links their nutrient-dependent hormone-organized and hormone-activated behavior to their pheromone-controlled physiology of reproduction.

Other examples of this "one big family" approach integrate what is known about the RNA-mediated cell type differentiation of crustaceans and insects. The other examples were included in: http://comments.s...6219.220

The research reports extended what we detailed in the molecular epigenetics of "From Fertilization to Adult Sexual Behavior" (1996) to what I detailed in my 2013 review "Nutrient-dependent/pheromone-controlled adaptive evolution: a model." Andrew Jones criticized the model, but did not provide another model for comparison.
JVK
1 / 5 (4) Oct 29, 2015
Re: "...criticized the model, but did not provide another model for comparison."

Like Vietvet (aka Steven Taylor) and many other antagonists, Andrew Jones (aka anonymous _9001) threw a tantrum.

Here is the response to his tantrum:

Editor's note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See also: Human expression QTLs are enriched in signals of environmental adaptation
http://www.ncbi.n...3787676/

Excerpt: "Environmental correlation is a way of detecting adaptation by testing whether the spatial distribution of the frequency of an allele could be explained by an environmental factor."

How could ecological adaptions be explained to serious scientists outside the context of environmental factors?
Captain Stumpy
5 / 5 (4) Oct 29, 2015
Editor's note

The 2013 review article by...
and the feedback from HIS bosses
hello harold,
So say what's hot in the paper ... kohl. or you will have to remove it,
or you pubie every forum against: it is also a way to
dismantle the pseudo science. j
bises
caroel
In other words... quit posting pseudoscience (except it was in french)
threw a
No, as Jones noted in the letter
Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published.
this is 100% accurate, from what most feedback has stated

repeating a LIE doesn't make it more true, little jimmie, any more than making unsubstantiated claims about links means you are correct (like you do above and WRT most studies you link)
Torbjorn_Larsson_OM
5 / 5 (4) Oct 29, 2015
"The regulars here may recall John A. Davison, who died in 2012. He was notoriously persistent and repetitive, and rather clueless ...

So he died, but you knew another had to emerge, and he has come. I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn't get it the first time, just say the same thing again, twice. A kind of sneering anger that people don't understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.

Behold James Vaughn Kohl. ... He's babbling in scientese.

And he just keeps hammering away with his pseudo-scientific pronouncements."

[ http://freethough...s-place/ ; from a _real_ biologist]
JVK
1 / 5 (2) Oct 29, 2015
PZ Myers ended his unprovoked attack when I cited "Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes" http://www.pnas.o...abstract

Excerpt: "...our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior."

His attack began with Davison's claims: "Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species..."

What these researchers now reveal via their ridiculous claim about 700 million year-old DNA is the fact they still know as little as PZ Myers about how nutrient-dependent RNA-mediated cell type differentiation is linked to fixation of amino acid substitutions in organized genomes via the physiology of reproduction, which is linked from the chromosomal rearrangements to pheromone-controlled behavior in species from microbes to man.




JVK
1 / 5 (2) Oct 29, 2015
Behold James Vaughn Kohl. ... He's babbling in scientese.


That claim is commonly made by biologically uninformed science idiots. See also: "I repeat: Octopuses are NOT aliens" http://scienceblo...-aliens/

This time, PZ Myers ended discussion with the claim: "New comments have been temporarily disabled. Please check back soon."

That was two months ago.The octopus genome sequencing linked the epigenetic landscape to the physical landscape of DNA via microRNAs and adhesion proteins linked to the supercoiled DNA that protects organized genomes from virus-driven entropy.

A video from the Mayo clinic confirms the link across all living genera in the context of precision medicine. https://www.youtu...youtu.be

A video from Baylor pokes fun at theorists, like Myers: https://www.youtu...youtu.be

All serious scientists laugh at his ignorance.
JVK
1 / 5 (2) Oct 29, 2015
Re: All serious scientists laugh at his ignorance.

See also: Human expression QTLs are enriched in signals of environmental adaptation http://www.ncbi.n...3787676/

Their review of biologically-based cause and effect was published two months after "Nutrient-dependent/pheromone-controlled adaptive evolution: a model." http://www.ncbi.n...24693353

It is much more technical, but they helped to confirm the facts I included in my model. Unfortunately, they failed to provide examples of ecological speciation, like the Nasonia wasps.

Fortunately, others have confirmed that my model extends across species from microbes to man by reporting that the bacterial flagellum re-evolved over the weekend. See my comment at: http://www.the-sc...ewiring/

No experimental evidence of biologically-based cause and effect supports the claims about 700 million years of evolution. Does it?
JVK
1 / 5 (2) Oct 29, 2015
See also the comments at: https://www.faceb...f_t=like

If you still want to claim that evolution occurs across 700 million years, see also:

Beyond species recognition: somatic state affects long-distance sex pheromone communication
http://rspb.royal...832?etoc

We linked ecological variation to ecological adaptation in species from microbes to humans by the nutrient-dependent RNA-mediated physiology of reproduction controlled by pheromones before the advent of sexual reproduction in yeasts, but moved forward from yeasts to link the conserved molecular mechanisms to humans. See: http://www.hawaii...ion.html

If my technical writings are too difficult to comprehend, see the general audience book I co-authored in 1995. http://www.amazon...9523383X

JVK
1 / 5 (2) Oct 29, 2015
Re: "If my technical writings are too difficult to comprehend..." -- as was obviously the case with PZ Myers -- See: Reviewed by Mark Sergeant: http://human-natu...ohl.html

Excerpt: A reader unfamiliar with olfaction research could come away from this text unaware of several key debates within the field, and take it for granted that humans do possess a functional VNO, and that the term pheromone can be applied legitimately in research concerning human olfaction. In short this lack of a critical approach undermines the validity of the book's contents. However it should be remembered that this book is aimed at a general audience, and as a result the authors may have felt it inappropriate to address the debates within olfaction research for such an audience. For a more academic consideration of the field by the authors, I would recommend Kohl's more recent review paper (Kohl et al, 2001), which addresses the issues outlined above."
Captain Stumpy
5 / 5 (1) Oct 29, 2015
unprovoked attack when I cited
you were banned by Myers for spreading hate & homophobia attacks... not for citing

this is not speculation, it is PROVEN
it is spelled out in your own words still on the site as well as admonished in Myers post #317
Mere stupidity I will tolerate, but I really don't need to give a platform to homophobes. Kohl has been banned
http://freethough...s-place/

your narcissistic Dunning-Kruger makes you believe the creationist diatribe you regurgitate so prolifically, and it also doesn't allow you to see actual science against your beliefs/religion, such as Lenski, et al... http://www.ploson...tion=PDF

reported for trying to link your homophobic argument here and being a chronic liar

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