Forum:DNA in amber

Let is have a discussion about the topic: DNA in Amber

Lebanorhinus specimen
I am now calling the Cretaceous weevil sequence into question. You said that Martin and Gutierrez may be wrong because the sequence only shows 98% similarity to modern weevils. However, I read their paper, and they said this.

From the GenBank database we retrieved 30 homologous sequences belonging to coleoptera and otherrelated insect groups (table 1) and aligned them using CLUSTAL W (Thompson, Higgins, and Gibson 1994).Maximum-likelihood pairwise distances (transition/transversion ratio52) were calculated with the programDNADIST (Felsenstein 1993). The outgroup was anodonate,Aeschna cyanea(X89481). Dipterans sequenc-es were discarded because of their high rate of nucleotide substitution (Friedrich and Tautz 1997). The dis-tance between the outgroup andLebanorhinuswas com-pared to the distances between the outgroup and otherinsects with a Wilcoxon nonparametric test. The difference was nonsignificant (p50.389), suggesting that theLebanorhinussequence is not ancient. The distance be-tween the outgroup and the fossil weevil was 0.130 andthe mean distance between the former and the other in-sects was 0.127.One might think that such a test would not discrim-inate a 120–135 MYA old sequence from an extant one; to counter that, we have estimated how much divergencewould have been lost by a 18S rRNA that stoppedevolving 120–135 MYA. First, as an estimation of the 18S rRNA substitution rate, we have used the estimatedmetazoan substitution rate given by Wray, Levinton, andShapiro (1996). For a period of 120 MYA, the expected divergence is 0.018. The mean distance between the out-group and extant sequences is 0.127; then, the distancebetween the outgroup and an 120-Myr-old sequence should be 0.109, the test now being significant (p,0.0001). We think that theLebanorhinussequence may bean extant beetle contamination. For instance, Waldenand Robertson (1997) recovered a beetle sequence when they were amplifying DNA from an amber-entombed bee specimen, but no coleoptera was studied before intheir laboratory.

I don't understand much of that, but I think what they're saying is that the Lebanorhinus specimen may have been contaminated by a modern beetle because the 18s rRNA gene doesn't have the expected amount of divergence for a DNA sequence that old. Did you consider this? And I did the BLAST again. The highest amount of similarity with extant beetles was 99%, not 98. I'm starting to think that it was indeed contaminated by an extant weevil, probably Hypera. I also heard that 18s rRNA is often used alone to make a tree because of how conserved it is. I made a tree again, and Hypera was indeed the closest relative. I feel deceived. User:Jurassic Park Treasury


 * I knew this for a long time, I've said what I think about it at the forum. Maybe we better discuss it here. There are two explanations for this:


 * There was no endogenous DNA in the weevil sample. Of all the insects, fungi and microbes it could have been contaminated with, it was contaminated with weevil DNA.
 * The Weevil DNA is from the Weevil sample.


 * I dare to say that unless you are biased against ancient DNA, explanation 2 in more likely. The sequence is very similar to modern DNA, but not identical. This DNA fragment was quite short, I dare to doubt how much we can extrapolate from it. The other fragment, probably from a symbiotic yeast, only had a 90% similarity with extant species. How do you explain that with modern contamination? BastionMonk (talk) 22:04, July 15, 2013 (UTC)

Correction: The yeast is 93% identical. However, you do have a point there. That sequence could be ancient.

But it isn't too far fetched that the prehistoric weevil could be contaminated be a modern one. Although you have pretty much zero respect for the critical studies of DNA in amber, you have to acknowledge that some contaminated sequences were actually from beetles. They could not have been from the amber insects because the insects being studied by the critics were bees and flies.

You asked me why this contaminated beetle wasn't sequenced by now. You have got to remember that DNA sequencing is not magic. We have not automatically sequenced every bug in existence. One of the Hypera sequences showing up in the BLAST list wasn't added until March 2013!

I am actually pretty divided on what to think. I want to believe in the ancient weevil DNA because it would be awesome. At the same time, however, my skeptic side is saying nay. I don't want to be wrong. However, even if it IS contaminated, it's not a complete loss, since the fungal sequence does seem ancient. Jurassic Park Treasury (talk) 01:37, July 16, 2013 (UTC)

Update: It seems that the only reason why the fungal sequence wasn't 100% similar to modern sequences is because the sequence has gaps. Otherwise, it only differs by 1 base pair. So the fungal sequence may be modern after all. Jurassic Park Treasury (talk) 04:22, July 16, 2013 (UTC)

Although you have pretty much zero respect for the critical studies of DNA in amber

I am actually pretty divided on what to think.

Don't get me wrong. I have respect for critical studies and stuff. I also don't know what to think. I KNOW something, or I DON'T know something. Is Cano's amber DNA endogenous? I don't know. I just dare to say that the case isn't closed. I am fed up the the global skepticism on paleo-DNA. Everywhere on the internet it says that DNA can't last longer than 100,000 years. However, DNA is extracted from 8 million years old microbes in Antarctic ice and a 700K years old horse's genome is fully sequenced. This shows me that the skepticism of the masses is unjustified.

If someone claims that it is proven that the Cano sequence is contamination, I raise doubts because the case isn't closed. If a group would claim the sequences are real, I would also raise doubts because I know there are indications it is not. I don't take sides, I only fight against those that take sides. You should do the same.

To be sure, we need a lot of more sequences from amber entombed samples. And I can't find reports about that. That could mean there is no DNA in ancient Amber, but I also can't find reports of DNA much younger amber or opal. So, I think there isn't much extraction done in the first place.

the only reason why the fungal sequence wasn't 100% similar to modern sequences is because the sequence has gaps.

Nice find! Gaps are even more unlikely to happen than substitutions. So, it CAN still indicate antiquity. BastionMonk (talk) 13:29, July 16, 2013 (UTC)

I was also wrong again. I looked at the fungus alignment again, and it did differ by more than one base pair.

From what I've heard, DeSalle also extracted DNA from amber wood gnats, but I can't find the sequences on GenBank or anywhere else, so I can't BLAST them.

"To be sure, we need a lot of more sequences from amber entombed samples."

Indeed. However, I doubt scientists will try anymore, thanks to Allentoft's DNA half-life study. Seriously, how hard is it to obtain some amber and attempt to extract DNA from it? Even if they fail, I doubt it would be much of a loss.

Jurassic Park Treasury (talk) 20:16, July 16, 2013 (UTC)

I did a BLAST search with the 18S ribosomal RNA gene of an ostrich. It only had a 1% difference to the chicken version of a gene, and they belong to different clades! The Lebanorhinus and Hypera differ by three base pairs, the chicken and ostrich differ by two. So the sequence similarity doesn't prove contamination after all. Jurassic Park Treasury (talk) 08:57, July 19, 2013 (UTC)

Reproducibility
One of the main points of Amber-DNA critics is that other teams couldn't reproduce Cano's results. I've not been able to find on what amber specimens they performed the extractions, but maybe this could be an explanation.

I stumbled upon this video of a amber-DNA critic:

Professor Timothy Rowe:

We have actually some insects in amber, and they're very misleading. When you look at ... this bug that is trapped inside the amber, it looks like a beautiful specimen. But the only parts of it that are preserved are the actual , its outer surface... When that animal was alive it had a inside, (when it died) it just digested it all out. So it turns out that when we section these things, they are hollow inside. There is nothing left, except the outer skin.

Now, we know that this isn't true in all cases. Poinar found Sandflies with the guts intact, complete with reptile blood. However, according to this professor the insects are hollow in most cases. When the insect dies, internal microflora digests the soft inside of the insect. After that they eat each other until nothing is left.

So, could it be possible that all those people that tried to reproduce Cano's results were actally trying to extract DNA from empty exoskeletons? If true, it is no surprise they found nothing. Maybe Cano and Poinar were lucky, because their Weevil had still some tissue inside it. BastionMonk (talk) 21:30, July 31, 2013 (UTC)