mrjonno wrote:About 4 billion years of course the DNA tends to get modified a bit through generations, my great grand daddy 10^100 or so was an little single cell

You'd probably need to downgrade the number of generations there a wee bit. 10100 is more than the number of planck times that fit into the total age of the universe.

It'd some short generations lol.

Well I assume most generations would be seconds to minutes but in life's very early stage (pre cell) it could have been a lot shorter

mrjonno wrote:Well I assume most generations would be seconds to minutes but in life's very early stage (pre cell) it could have been a lot shorter

But not nearly that much shorter.

The universe is about 4.354 × 1017 seconds old, the Earth is just 1.439 × 1017 seconds, and life itself about only 1.12 × 1017 seconds.

To fit a googol of generations into that would require fairly short generations indeed. On average, 1.12 × 10-83 seconds each. That's so much less than the Planck time; of 5.39106(32) × 10−44 seconds.

Ok fair enough 10^100 was a bit of an exaggeration but DNA is potentially immortal but its carriers alas are not

And bang on cue we have this report:

Ancient Yukon horse yields oldest genome ever
700,000-year-old DNA reveals history of horse evolution
<snip>
However, different kinds of proteins remained preserved in the bone, making other scientists optimistic about the possibility of it yielding useable DNA.

In the end, using new technology, researchers were able to do what many would have thought to be impossible.

"All of the tiny bits we were are able to piece back together and reconstruct informatically the entire genome," Orlando said. It wasn't easy — Orlando said only one out of 200 DNA molecules sequenced by his team belonged to the horse. The other 199 belonged to bacteria that colonized the bone after the horse died.

But once the task was complete, and the ancient horse's genome was compared with that of the only living wild horse species, the Przewalski's horse; modern horses; and donkeys, the team learned a lot about horse evolution.

http://www.cbc.ca/news/canada/north/story/2013/06/26/science-ancient-horse-yukon.html
The only remaining refuge for scoundrels is in radiometric dating denial.

mrjonno wrote:Ok fair enough 10^100 was a bit of an exaggeration but DNA is potentially immortal but its carriers alas are not

Unless of course you count bacteria. They just divide in two to reproduce. Plus, thanks to horizontal gene transfer, they can pick up useful genes from their neighbours, integrate said genes into their own genomes, and bolster themselves against incoming threats in a manner that isn't available to you or I.

Oeditor wrote:And bang on cue we have this report:

Ancient Yukon horse yields oldest genome ever
700,000-year-old DNA reveals history of horse evolution
<snip>
However, different kinds of proteins remained preserved in the bone, making other scientists optimistic about the possibility of it yielding useable DNA.

In the end, using new technology, researchers were able to do what many would have thought to be impossible.

"All of the tiny bits we were are able to piece back together and reconstruct informatically the entire genome," Orlando said. It wasn't easy — Orlando said only one out of 200 DNA molecules sequenced by his team belonged to the horse. The other 199 belonged to bacteria that colonized the bone after the horse died.

But once the task was complete, and the ancient horse's genome was compared with that of the only living wild horse species, the Przewalski's horse; modern horses; and donkeys, the team learned a lot about horse evolution.

http://www.cbc.ca/news/canada/north/story/2013/06/26/science-ancient-horse-yukon.html
The only remaining refuge for scoundrels is in radiometric dating denial.

From that news article:

Over time, some parts of the genome that showed the biggest changes were the genes that control the ability to smell and the animal's immune system.

This of course, is entirely consistent with evidence from modern day speciating lineages - the genes that undergo the most rapid changes are olfactory genes and genes for the major histocompatibility complex, the proteins that form the foundation of the immune system. And in the case of the fertillin gene subset of the latter, form the foundations of interfertility.

EDIT: the paper is in Nature. News article in Nature itself here, actual paper here.

Sadly the paper is behind a paywall (again), but the abstract is as follows:

The rich fossil record of equids has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr BP)2, 3. Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus4, 5. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population6. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Calilasseia wrote:Sadly the paper is behind a paywall (again), but the abstract is as follows:

The rich fossil record of equids has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr BP)2, 3. Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus4, 5. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population6. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Cali, Do you know of any studies made of the relationships between present domestic horse breeds? For example, are there any breeds which are particularly distinct and genetically uniform from others, which may have evidence of a lot of recent crossbreeding.

My friends at the Rare Breeds Survival Trust would probably like to know. They were involved with a recent similar study about the relationships between chicken breeds at Roslyn, Edinburgh, in which my former (I can't keep cockerels where I live now) favourites, the White-Faced-Black Spanish came out as most uniform and distinct.

Not off the top of my head. Though I suspect if you contact the editors of various scientific journals, asking them if they have any papers on equine genetic diversity, they could prove most helpful. A quick Google Scholar search on "equine genetic diversity" brought up this paper, if that's any help.

Thanks for that. I'll pass it on the RBST.

Edit to add:

I've passed it on to the general genetics person at the RBST, and she has passed it on in turn to their main horse genetics advisor.
She also sent me a link to this project which the RBST is helping with:

http://www.uky.edu/Ag/Horsemap/abthgp.html

On the OP, From what I remember there is still a question of contamination with the osteocytes. The lab in question had preformed similar tests on extant avian dinosaurs before the test and found similarities to the extant avian dinosaurs that the lab tested before. The question of contamination must come up.

I think Schweitzer's lab addressed that.

Yes, from memory they used multiple different assays to ensure that they were covering the bases on the source material. They ran phylogenetic analyses on amino acid sequences that showed that the hadrosaur collagen was closest in sequence to chickens, IIRC.

Heh, chicken.

Can you imagine if Tyson Foods® managed to re-sequence Hadrosaur genome, inoculated sterile chicken eggs and farm raised 4 ton birds?

A whole new way to strip tropical rain forests!


I think I've talked about this before, but what the hell, I'm off work today.

I have seen, held and smelled small pieces of amber from the thin coal seams in the eastern Hell Creek formation, Firesteel member.

Attempting to preserve these hyper fragile specimens was among the most frustrating of my field experiences. The longer they were exposed to air the more brittle they became, and unless sealed in a air tight container, preferably charged with an inert gas (like Argon) would become so much sand-like shit. However just freeing these things from the coal seams was like lifting wet tissue holding shattered glass together. We were afraid that any preservatives/stabilizers would dissolve these little sheets of jewel. Ultimately we choose to save sections of coal for more controlled work back at our prep lab.

To me these fragile specimens smelled like western (usa) red cedar Thuja plicata (wiki) when being sawn or milled.

I've also seen what crotards call Polystriate Trees in the same formation. Apparently a huge ashfall encased a finger of timber in a fully upright position. Subsequent erosion and deposition had left the stumps above the surface of a varied sediment load. However the roots were limited to a layer that had significantly different characteristics from the varied horizons encasing the trunks. This root layer was much like what one might expect to find in an extant wild forest, and consistent with a stable environment. These trees had a fibrous quality, and also smelled of cedar when bruised. Unfortunately these trees lie on private land, and that one short day of non-collecting examination was all I was allowed. I'm sure they stand as I last saw them, as the owner had no desire to allow any lasting disturbance.

I know these trees were actually Dawn Sequoia, Metasequoia glyptostroboides (wiki).

The point of all this is to highlight that the type of depositional settings found within the Hell Creek (and probably many other late Mesozoic formations) has the potential to preserve in exquisite detail, and maybe, with enough testing we can find sufficient fossil DNA to answer a few questions. One I'd like to see addressed would be;
"Does hadrosaur DNA display any genetic clues as to their metabolic state?"

I'll probably have to wait a good while for any reasonable answer to that.

That question has been beaten to death, and we still, really, can't know if SAURISCHIA or ORNITHISCHIA were both, either or neither "warm Blooded".

Perhaps new field work needs to be done with downstream genetic testing in mind, and limit the pollution of samples as much as possible, maybe using charged sealed containers.



Of course, being a man that would much rather walk over a bentonite flat than sit at the prep bench, I feel that initial documentation and collecting is THE most important step in the process. An idiot can fuck up a world heritage site, and a pro can bring the world stuff like this quest to push our knowledge, and testing methods, even further. Nothing but good can come from this.



RS

Metasequoia glyptostroboides Ah, that takes me back to plant identification classes. This was one of the most tongue twisting plant names and therefore often in tests. The opposite arrangement of the needles on the twigs was an identifying feature which could be used in fossil finds of the plant itself, scent is often an identifying feature too for fresh live specimens, but I never thought you could identify the species of tree that a geological find of amber came from by scent. I have often licked and chewed rocks to aid identification but never sniffed them.

Freshly exposed rock surfaces, like after smacking one open with a hammer, will often release gases trapped therein. Some rocks really stink of sulphur and others smell like dank swamp. I imagine that with some testing the chemicals could be deliniated from the solid material in the rock. That's sortta what happens with hydro-fracking in shale formations and methane is released.

RS

What are the optimum natural conditions for sustaining DNA?

Cold, I would imagine, James. Dry cool caves have also yielded old DNA.

There was a recent study of a Canadian wild horse from about 700K years ago that the entire genome was recovered. That's a whole bunch short of any Maastrichtian fossils though, and was found in permafrost that has not significantly thawed since the horse was originally frozen.

LINK

RS

jamest wrote:What are the optimum natural conditions for sustaining DNA?

Those what is found in living cells.