When DNA analysis is done and it comes back as Human DNA or contaminated with Human DNA, do they specifically mean Homo Sapiens, or just Human in general? Is there a significant difference between say Homo Sapien and Homo Neanderthalensis DNA that it would jump out and be very obvious, or would further analysis/testing need to be done to differentiate between the two?

They mean modern humans because it would be easy for us to contaminate the sample. It would take a fairly long sequence to see the difference between a modern human and a neanderthal. I understand that it is common to do the mitochondrial analysis with hundreds of base pairs and that would probably be more than enough to tell. If it was verified and actually as distantly related as Neanderthal, it would be a big deal.

There is about 9% difference between humans and Chimps on the mitochondrial DNA sequence. You would probably get about 1 percent difference on the Neanderthal because it was reported to have a common ancestor with us about 600,000 years ago and that is 10 times more recent than the common ancestor with a chimp. You can see why you would want to have several hundred base pairs if something were that close. You would be only averaging about one change per hundred base pairs sequenced. Random chance could reduce that on a short sequence.

BobZenor, thanks for sharing your knowledge of this element of research. It's so common for us lay-people to ask, 'why not extract DNA from scat/hair etc. and find out what this thing is?' Your posts have gone a very long way to explaining why that doesn't happen.

However, if you're so inclined, would you answer a few questions so I can get the DNA thing totally sorted in my mind? I'd be very grateful.

1. Given that hair and scat samples are the only physical parts of this animal you can take away and analyse, will DNA analysis of these always be something of a dead-end?

2. Am I right in thinking that in the past analyists have observed DNA so close to being human that they've had no hesitation in labelling it human? Perhaps even suggesting contamination as a reason?

3. How useful would blood samples collected from the ground be as regards DNA samples?

4. I get the impression that the approach to sample analysis is haphazard and disjointed. Do you think BF research is missing a trick by not having a centralised process whereby all samples are examined by the same people, undergo the same tests and the results of these stored on the same database where they can be catalogued, photographed and compared? And, regarding hair samples, isn't detailed photography at least as important in terms of matching samples from different areas?


As you'll see form these questions, I, like many, place a lot of stock in our ability to analyse DNA, but have little understanding of what that actually entails. I'm keen to expand my understanding, but I also believe that people as a whole trust DNA analysis, having heard of numerous forensic crime scene events etc. So, final question -

5. If a clear, well-funded and concerted effort were to be made regarding hair (and maybe scat) analysis, what's the best that we could hope for? Could we ever claim there's enough evidence to strongly support the theory that an unknown creature occupies much of North America?

I hope you don't mind the list of questions - I have a feeling that the answers might enlighten more than just me.

Ludo

I will give a brief description of the main DNA test so you might have an easier time visualizing what is going on. That would be sequencing the mitochondrial DNA. Mitochondria are basically in all tissue and it also can be sequenced from hair that hasn't been exposed to the elements for a long time. Mitochondria have a small amount of DNA that is like the DNA of bacteria. The host cells control the growth of mitochondria so they aren't completely autonomous. They supply energy to the cell like thousands of fuel cells. They have a section of DNA on their single circular chromosome that doesn't code for proteins so any change to that region doesn't affect the ability of the mitochondria to reproduce. That theoretically means that mutations will occur randomly on that section of DNA that is something like 2500 base pairs if I remember correctly. They simply sequence part of that region and compare it to other animals based on the number of differences. The longer your sequence, the more precise the analysis is since the mutations happen randomly over time.


I imagine scat would have to be very fresh.
Testing a long sequence of mitochondrial DNA would almost certainly show an animal between two different kinds of apes. The most likely result IMO is something between a modern human and and a chimp. There is a small chance it could be very close to a modern humans or be a hybrid and the test would show modern human. That would make it unlikely to be distinguishable on a normal analysis but I really don't think that is at all likely. It is not logical for BF to be so close to another animal that the analysis would have a problem distinguishing a new species of ape. It would be near proof of an unknown ape, assuming it was verified, and likely an unknown hominid and you could tell how closely related to humans it was. That isn't anything like unknown primate. You would know what it basically was. You don't really need an animal to compare it too because you have humans and chimps and a variety of other apes to compare it to.


That is correct but there are various kinds of tests and they don't all mean the same thing. Sequencing the mitochondrial DNA can distinguish individual modern human populations now. Older tests and other kinds of tests could only see it was a primate or something close to humans. Bigfoot, from a theoretical biological point of view, could easily be only a few hundred thousand years since we shared a common ancestor. That would require a very long sequence to see. It is possible from a biological point of view for an animal to evolve that quickly but it is very unlikely in my opinion. That is the major weakness of the DNA analysis. An intact sample should probably be easily distinguishable since they probably aren't that close to us.

They add DNA replication enzymes and any human microscopic flake of skin could have the DNA amplified millions of times over and contaminate the analysis. That would come back as modern human. I am not that familiar with how they perform the analysis exactly but the tiniest amount of human DNA could show up. That is why they are quick to assume contamination.


That could be extremely useful if it were fresh. You would have nuclear DNA and that would make it a much higher level of proof.


I don't think it matters if we have a central database. There is already a database that lists all the animals. If something comes back between a chimp and a modern human, it would be earth shattering if they verified it. They wouldn't call it unknown and there would be no chance of that getting lost. Something really close to a modern human might get lost or not noticed but again that seems unlikely.

I don't mind. I love to type and it is no effort.

If we found a couple of hair samples from multiple locations that were closely related to each other but half way between a chimp and a human, it would be near proof of their existence. That would open the door to big money being made available to find them. They couldn't evade an all out government sponsored effort for long. That DNA would be widely sought out if it turned out to be between a chimp and a modern human. They would probably need to add protection fast.

Bob, you are a scholar, a gentleman and a star. Thank you for the answers.

Ludo

I have another question for Bob Z or others in the know. After finding the report below I
am wondering why it is not considered as a possible answer to the Sasquatch ancestry
question. Has it been proven to be a fabrication, or ignored because of the source, or
some other reason?

"In total we generated 328bp of mitochondrial sequence. The next step was to ask whether this actually was ancient DNA, and if it was, how does it compares to modern human DNA and previously isolated Homo Erectus DNA. This case was especially important, as we had generated relatively long PCR products from an ancient non-permafrost sample. Radio carbon dating of the sample dated it to 29,000YBP (roughly 30,000 BC) (K. Liden); therefore, products greater than 100-150bp were not expected.
COMPARISON TO MODERN HUMANS The first part of the analysis was to compare our aDNA to the Cambridge Reference Sequence (CRS) (4). The two sequences were aligned and any base substitutions, insertions or deletions were recorded. Figure 2 shows one of the cloned PCR products in comparison to a modern human mtDNA identical to the CRS's hypervariable region I showing one insertion and one substitution: in total there were 22 substitutions and one insertion. When comparing any two modern Europeans, the average number of base substitutions over the equivalent region of mitochondrial sequence 5.28 +/- 2.24; therefore, the level of variation between obtained from the Homo Erectus and the CRS was extremely high. This high level of differentiation was seen in a larger scale comparison to 300 modern European sequences with an average number of substitutions of 23.09 +/- 3.27. Similar results were obtained when the sequence was compared to modern Asians and sub-Saharan Africans: 23.27 +/- 4.06 and 23.09 +/- 2.86, respectively. Based on these results, it appeared that the DNA extracted from the rib was not closely related to any modern mtDNA.
CONCLUSION Analysis of the aDNA sequences showed two things. First, the DNA recovered from the “Skeletal finding” Site was very similar to the Sanders Site and has subsequently been shown to be similar to the Topper Site samples. Therefore, it can be concluded with a high degree of confidence that Homo Erectus DNA has been recovered and that this in not some kind of peculiar contamination. Second, the Homo Erectus DNA is significantly different from modern human mtDNA, forming a distinct group. These results indicate that Homo erectus contained a distinct type of mtDNA. While it is not possible to know whether Homo Erectus and modern humans did interbreed, based on the Homo Erectus and modern humans analyzed to date, it is possible to conclude that Homo Erectus did not pass any of their mtDNA on into the modern European mtDNA pool. Further analysis of Homo Erectus DNA will provide information on the molecular diversity of Homo Erectus."

If you mean has it been considered that Homo Erectus could be the ancestor to Sasquatch, the answer is yes. Not everyone is so sure it's just an ape, albeit a BIG APE.

Homo erectus or more likely something close enough to be cataloged as belonging Homo erectus has been my favorite candidate as the most likely ancestor. We now have floresiensis that indicates a much more primitive lineage of hominids likely lived in Asia. Some of the "erectus" were likely more "primitive" than supposed. There is good evidence for erectus being multiple species. .

That was a confusing article about the erectus being compared to modern humans. I have never heard of them sequencing mitochondrial DNA from erectus. They did it for Neanderthals. There are only a few fossils that I heard of that were recent enough. That is really recent for erectus and them getting mitochondrial DNA?. That is really interesting and I am surprised they aren't making a big deal about it or at least that is the first I am hearing about it.


After trying to find the two archeological sites mentioned, I found several bigfoot related sites. This one involved Biscardi and some old skeleton he found. I remember how something about that didn't go over so well with an Anthropologist on this forum several years ago but I don't remember why exactly. Messing with graves is a touchy subject. The guy has a history of exaggerating the truth. I am assuming for now that the DNA data is taken out of context because several things about it don't add up.

Bob, wouldn't there be a procedural protocol in place to cleanse a hair sample in some way before sequencing? Obviously a sample collected in the wild would have potential contaminates from the surrrounding environment, so why they would test a sample without some cleansing is beyond me, and this should certainly be able to remove any flake of human skin.

SY.

A couple things for clarity:

Mitochondrial DNA is not referred to as being on a "chromosome" (which would make it nuclear or at least confuse the issue).

DNA can be recovered from samples that aren't particularly fresh (e.g. at least tens of thousands of years)- in all depends on what environmental conditions the samples "experience," but fresher is generally always better.

Reminder of the Skwiki entry. Maybe you can add some of the mtDNA discussion Bob?

-A

I was wondering about that when I chose the word. It seemed like I remembered bacterial loops of DNA being called chromosomes but I could be mistaken. That was a long time ago that I am remembering. I had to think about that and couldn't come up with a more suitable word. Even if I read that, it doesn't mean it was an appropriate use of the word so I appreciate the correction.

No problem Bob and I hope you know your efforts are appreciated by all of us.

That is beyond my experience. I do remember an article about very ancient hair tens of thousands of years old found in a cave. They did talk about cleaning it with bleach to remove the possible contamination, since it had been handled, before they dissolved the hair and performed the analysis. It is something they could do but I don't know their procedures well enough to know if that is normal. I was wondering the same thing when it comes to contaminated hair analysis.

Samples such as blood and tissue collected in the field should be collected with extreme
sterile methods to prevent contamination.

However, the dna contained within hair is protected by the keratin from contamination. As
long as the hair is cleaned before testing, any contamination would have to occur in the Lab
after cleaning. Following is a simplified explanation of the cleaning:

"DNA analysts clean evidentiary samples prior to the mtDNA sequencing process to remove contaminating materials surrounding or adhering to the sample. This step ensures that the sequence of the DNA obtained from the sample originates from the sample and not from exogenous human DNA.
The cleaning process for hair samples uses a detergent treatment in an ultrasonic water bath, which removes possible contaminating residues from the hair. The hair sample is then placed in an extraction solution and ground using a small mortar and pestle, resulting in a mixture that contains both the cellular material and the released DNA."

Very true, and I echo the sentiments!

Just a point of clarity...bacteria contain a single circular piece of DNA also referred to as a "chromosome", where as we have a set of more or less linear "chromosomes". The nuclear chromosomes in eukaryotic (animal) cells undergo replication and segregation during mitosis, but replication of mitochondrial DNA is performed independent of cell division and is partitioned as the mitochondria are split between the two new cells. Still Bob, very good answers above.

Thanks for all the kind words. All I meant when I said it wasn't completely autonomous what that many of the genes that are used by the mitochondria are held by nuclear DNA in the host cell. I understand why some have remained in the mitochondria and it might have something to do with how the genes are activated or regulated by something in the metabolic process of the mitochondria. What seems relevant to me is how there is apparently some sort of balancing act going on because mitochondria don't evolve independently. All humans share the same haplogroup (hopefully the correct word) from the so called mitochondrial Eve 170,000 years ago. That suggests there is a selection that involves some balance between the nuclear and mitochondrial DNA. Otherwise mitochondria wouldn't be specific for species. It is just a really huge puzzle to me how animals go to quite a lot of trouble to maintain a specific mitochondria. They mark the mitochondria in the sperm for destruction. Why is that an advantage. Why not just let the mitochondria evolve on their own. Something is going on that I haven't figured out yet. I was just alluding to that and didn't mean they didn't divide on their own. I just didn't want to suggest they were like some bacteria that was on its own dividing in the cells.

Sorry about the typo in the second sentence. I have a strange problem where I read what I was thinking when I typed it and not what I actually typed. Editing my own writing is hard because of that.

"Analysis of human hair at a crime scene may be possible with a portable technique adapted by Queensland University of Technology researcher Sarina Brandes.
The technique, called Near Infrared Spectroscopy (NIRS), has the advantage of being readily available and Ms Brandes has demonstrated it could be used to analyse hair for forensic purposes.
A chemistry Masters researcher, Ms Brandes said this method was independent of analysis of DNA, which could break down quite quickly, especially at disaster scenes such as after a tsunami.
Her supervisor, Dr Serge Kokot, who has researched the forensic possibilities of human hair analysis for the past 12 years, said human hair could survive relatively harsh environments, where DNA couldn't.
"NIRS has been found to need only a few millimetres of a single hair for analysis, but until now, we have not had the ready capacity to apply this technology in harsh environments," Dr Kokot said.
"Ms Brandes' achievement is several fold: it opens the door for on-field measurements; it provides a method for analysis of hair after immersion in water, and it also has the advantage to readily differentiate a naturally coloured hair from that treated with a hair dye to give a similar colour."
Dr Kokot said Ms Brandes' technique could obtain the infrared profile from only a tiny part of a strand of hair and then interpret this profile using specialised mathematical methods to compare it with similar profiles collected from suitable reference hair samples.
"The results can be displayed in an easily understood diagram and/or the profiles can be rank-ordered and the position of the tested hair can be established relative to the reference samples," he said.
"In this manner, Sarina's technique can establish a person's gender, race and whether they had chemically treated their hair, as well as what the original hair colour was."
Dr Kokot said the use of Ms Brandes' research could help to identify victims of natural disasters, like tsunamis, where hair has been in water.
"Other useful spin-offs have been that Sarina's technique can also identify what type of water the hair was found in, like sea water, and how long the hair had been immersed in it," he said.
"Hair found at a crime scene could be matched against hair found in a comb of the victim which can be used as the reference sample, or it can be compared against hairs from suspects in a similar manner."
Dr Kokot said portable NIRS instruments were available and could be used at a crime or disaster scene.
Contact: Rachael Wilson, QUT media officer, 07 3138 1150 or rachael.wilson@qut.edu.au.
Source: Queensland University of Technology"

Interesting development on the NIRS.

Its an intriguing question. I think most of the time the labs that analyze DNA in the US are looking only for a difference in the mitochondrial plasmid DNA between modern humans and modern great apes or other known animals (such as opossum, lol). I don't think that there are any labs in the USA (except perhaps the biochemist Geoff Meldrum is working with) who can differentiate the minute differences in mtDTA that would be present in the samples if they are in fact from a relic upper level hominin such as a Homo heidelbergensis or Homo erectus.

I mean, it is only fairly recently that a sample of Neanderthal mtDNA has been extracted, isolated and compared to modern mtDNA and to the mtDNA from one other Neanderthal,

http://www.talkorigins.org/faqs/homs/mtDNA.html

This article is a good overview of this whole area of study, by the way.

As far as I know the only lab that is doing the fine differential comparison of hominin DNA is that one in Germany. It is no wonder that people are getting DNA analysis lab results which label their submitted DNA as "human" or "human contamination" if what they are expecting to find is something from a great ape.

A possible complication if Bigfoot is found to be a relic hominin is that of interbreeding with modern humans, as has been postulated. We know that close species of other animals are sometimes able to interbreed and it is not an impossibility genetically speaking. If bigfoot exists and is actually, for example, Neanderthal or Homo erectus, and has as a species abducted or interbred with human females, they could even have mtDNA that shows up as completely modern in lab tests! Now that would be a doozy of a finding and a real monkey wrench in the research process.

So the upshot is that not only mtDNA should be tested for but also Y-chromosome testing done too. And ultimately the best thing would be to get live tissue and do a chromosome count, as we know that humans have 23 pairs of chromosomes and great apes such as chimps have 24 pairs. Most big city medical centers are able to do a chromosome count, all you need is a photomicroscope that can take large enough images of chromosomes in the act of meiosis, present in most stained cheek or mucosal cell samples. The corker of course is getting a live cell sample or cheek swab from a living BF. Where's Fox when you want him? LOL

http://www.gate.net/~rwms/hum_ape_chrom.html (a rather interesting article on this having to do with questions of origins)

"monkey wrench"

Don't mean to take this off topic; itis an endlessly interesting subject lately as the technology and theories behind the actual workings of living stuff increases to the point where we might actually make some remarkable discoveries. I don't pretend to understand half as much as I wish, and I wonder just what the heck we really do know for sure. And why should we think otherwise when it's so darn complex.
Never the less, the other day I stumbled upon something that was pretty amazing, if you're curious about the state of the art when it comes to what we know. Last week the "discoverer" or "de-coder" of the human genome, Craig Venter and his collegue George Church (possibly the highest calibre authorities on genetics today) conducted 6 hours of lecture to a select group of interested parties including Google's CEO and co-founder Larry Page, Microsofts chief technologist emeritus Nathan Myrvold, a number of "serial entrepreneurs" with significant achievements in high tech, Stewart Brand of the Well and founder of the "whole earth catalogue", renown epidemiologist Larry Brilliant (founder of SVEA foundation) George Dyson (Freeman's son)...and a dozen or so other interested parties.
The lectures were recorded and are online at the Edge.

http://www.edge.org/3rd_culture/church_ven...er09_index.html

The level iof discussion s high, but you know that the target audience, as smart as they are, are in some ways no better informed in this than we might be if we stretched it some.

Great link! Lots of stuff to dig around there, like this one:

http://www.edge.org/documents/life/Life.pdf

Anyway, just an aside about mitochondria in mammals for BobZenor, the only reason mitochondria come solely from the mother's egg and not the sperm is because mitochondria are cellular organelles and exist solely in the cytoplasm (not the nucleus) of the cell. Sperm shed their cytoplasms during their development, in the interest of greater mobility. The egg, on the other hand, keeps its cytoplasm. So everybody's cells have inherited the cytoplasms of only their mothers, including all the cell organelles such as the mitochondria. There's no special reason other than economy of motion for those little sperm, they need to be tiny and fast. If you are referring to some other research, let us know!

(however it is true that sperm keep a few mitochondria wrapped around the top of the flagella to power them along, but these are shed, with the flagella "tail" when the sperm enters the egg.)

The point I was alluding to was kind of esoteric and it was why are mitochondria specific to species. They divide on their own like bacteria so it would be natural to assume they are independent.

wikipedia

I just meant that as an example of how something is going on where the species seems to be trying to control variation in mitochondria. There could be other reasons why male mitochondria might be automatically rejected but why would the embryo go to the trouble of destroying the male's mitochondria? They could be better than the females. It seems strange that mitochondria would be so specific to a particular species. I assume that much of that comes from the classic definition of species where it defines species as animals that interbreed but there could still be very much greater diversity in mitochondria. There seems to be some unseen mechanism that makes it more species specific than I would expect. All other lineages or haplogroups of mitochondria that existed in our ancestors before 170,000 years ago have been eliminated by selection. That is very powerful selection pressure.

Could it have something to do with the varying species-specific requirements for organisms to have "particular" rates of metabolism or particular needs in terms of "engine"
size? Is the ubiquitin then helping the male mitchondria to undergo some form of apoptosis? That is a good question why? Sparing and paring and specialization is a basic neuronal strategy in development, possibly it could be something as simple as economy of space. There would seem to be something else operating but what? Also, with accidents of development I would wonder what would happen if some of those mitchondria from the male "stow-awayed" to the egg?

Hi all,

I would like to know what you make of the following statement?

"We found some DNA in it, but we don’t know what it is. It’s not a human, not a bear nor anything else we have so far been able to identify." This quote is from Dr. Bryan Sykes at Oxford after testing DNA in a hair said to come from a Yeti in Bhutan.

To me, this does not make sense. He has DNA but he will not disclose which animal it is most closely related to! Why would he do that? Could you really have unknown DNA and not be able to place it on the evolutionary tree? This is just unbelievable...They spend good money to go to Bhutan, find a local tracker who takes them to a sighting location, find a hair, do a DNA test, find unknown DNA in the hair, and then just give up and drop the ball!!! How can this be?

According to Dr Meldrum's book Sasquatch: Legend Meets Science they were unable to sequence the DNA. That is rather vague about why that happened but they apparently didn't get any sequence at all. I would think it likely that there was only bacterial DNA and nothing from a higher mammal. I believe they have universal primers that select a section of mitochondrial DNA that are "universally" conserved in the mitochondria and sequence from there. They might not have the correct one since they were looking for a bear but I don't know how specific universal primers are. I would think they are probably specific enough to target all higher mammals. There probably wasn't any mammal DNA in the hair. They make it sound like it is the first time they have DNA that they couldn't get a sequence off. I would think it would be common if they tested samples that didn't have vertebrate DNA. It is hard to know what they did since they seem to want to sound mysterious about it.

I think this is the same case you are referring to.
They did not disclose it simply because they did not have the matching dna in their data bank,
and did not know what it was. Later tests showed the following:

"By Alastair Lawson
BBC News

The goral goat - it took several scientific tests to make the connection
Scientists in the US who have examined hairs claimed to belong to a yeti in India say that in fact they belong to a species of Himalayan goat.

They say that DNA tests on the hairs - obtained from the north-east Indian state of Meghalaya - show that they are from a goat known as a Himalayan Goral. "

BobZenor, thanks for the information. I had not heard that they were unable to sequence the DNA. I'm still a bit surprised that an Oxford DNA expert would say, "It’s not a human, not a bear nor anything else we have so far been able to identify." for something he could not sequence. I guess he was trying to keep people wondering instead of explaining his findings, or lack of.

Olmanothewoods, the sample I am eluding to came from Bhutan, not India. Here's a link to the story.

http://www.newscientist.com/article/dn583-mystery-beast.html