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Author Topic: Calibration of TMRCA extimates with Delta 14C data  (Read 859 times)
spanjool
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« on: July 01, 2012, 01:43:04 AM »

There has been a intensive discussion about the quality of TMRCA estimates. It has been looked into through theoretical considerations and reflected against historical informations more or less backed up by empirical research. Carbon and isotopic dating artefacts associated with past populations gave us time lines to hold against these TMRCA calculations.

In genetic genealogy we use the SNPs indicators for speciation events while the diversity of the STR based haplotypes is seen as anagenetic developments within monophylitic clusters.

By excluding the multi and fast markers in the STR based haplotypes an effort is made to replace the SNP based synapomorphic characters with sets of STR markers and in doing so we come to a TMRCA estimate.

The mechanism of the variation in the VNTR is (mostly) DNA replication slippage while SNP is the consequence of a fixed mutation caused by external influences such as metabolic stress and/or ionising radiation. STR events are more or less internal; SNP novelties have external causes.

Radiation pressure causing ionising effects is reflected in the Delta 14C data as published by the International Carbon Calibration curves (http://www.radiocarbon.org/IntCal09.htm).

I constructed two graphs: first an graph in which the the SNP count (irrespective of its haplogroup) is set against the estimated TMRCA (data supplied by Marko Heinila).
https://dl.dropbox.com/u/74936451/SNP%20count%20%204-5.3.pdf
In the second graph the Delta 14C is plotted against the calibrated age (ybp).
https://dl.dropbox.com/u/74936451/delta%2014c%20versus%20ybp%204000-5200.pdf

I used the period from 4k till 5.3K for these graphs.
If the appears to be an interest in his approach I can make available the graphs of the whole period between present and 20K years ago.

Hans

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alan trowel hands.
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« Reply #1 on: July 01, 2012, 10:12:38 AM »

Thats interesting stuff.  However, can you expand and comment on what you think this means for TMRCA estimates in plain language for folk like me who can barely count.
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acekon
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« Reply #2 on: July 01, 2012, 10:25:44 AM »

I'm also not the sharpest tool in the shed, and was also wondering how we can use the TMRCA play thing with unknown and or  undiscovered  conjectured ydna groups? 
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razyn
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« Reply #3 on: July 06, 2012, 01:49:10 PM »

The mechanism of the variation in the VNTR is (mostly) DNA replication slippage while SNP is the consequence of a fixed mutation caused by external influences such as metabolic stress and/or ionising radiation. STR events are more or less internal; SNP novelties have external causes.

Radiation pressure causing ionising effects is reflected in the Delta 14C data as published by the International Carbon Calibration curves (http://www.radiocarbon.org/IntCal09.htm).

I'm refreshing this conversation because Hans at least knows what he's talking about, and it's important.  Alan asked for plain language.  I suspect that the "plain language" required in this case is English, not translated from Dutch, and not from the mind of someone who is professionally familiar with the terminology of genetics.  So here is my attempt at that:

There have been recent efforts to calibrate TMRCA estimates with events, the dates of which are known from non-genetic sources (such as history, archaeology and linguistics).  It may be profitable also to calibrate them with external events that cause genetic stress and lead to mutations (SNPs).  A leading class of candidates for such events would be the spikes in background radiation that are reflected in the table of Delta 14C (itself a combination of evidence from tree rings, coral rings, and marine sediments), published in the 2009 study at the first link posted by Hans, and quoted above.

And on the assumption that that might be a good thing to do, Hans has done it:

Quote
I constructed two graphs: first a graph in which the the SNP count (irrespective of its haplogroup) is set against the estimated TMRCA (data supplied by Marko Heinila).
https://dl.dropbox.com/u/74936451/SNP%20count%20%204-5.3.pdf

In the second graph, the Delta 14C is plotted against the calibrated age (ybp).
https://dl.dropbox.com/u/74936451/delta%2014c%20versus%20ybp%204000-5200.pdf

I used the period from 4k to 5.3K for these graphs.  If there appears to be an interest in this approach, I can make available the graphs of the whole period between the present and 20K years ago.

Hans

I have had the impression that Hans is disappointed in the perceived lack of interest in this, by members of our forum.  Maybe it is more a lack of familiarity with his terminology; or even with the concept that spikes in cosmic/solar background radiation may be responsible for genetic phenomena we have been correlating with more specifically terrestrial events (such as migration, invasions, epidemics, volcanic eruptions, floods, and climate change).

Anyway I find it interesting, provocative, and worth doing... by somebody else (for example, Hans) who knows what he's doing, and understands why.

Before writing this, I looked up some of his terms, in online dictionaries or Wikipedia, and found that also to be a pretty interesting exercise:

http://en.wikipedia.org/wiki/Synapomorphy

http://en.wikipedia.org/wiki/Variable_number_tandem_repeat#VNTR_structure_and_allelic_variation

http://en.wikipedia.org/wiki/Short_tandem_repeat
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ironroad41
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« Reply #4 on: July 09, 2012, 07:39:22 AM »

 These are two emails I shared with Neil McGregor re: a paper Jean L referred to re: gene expression.  I think his comments are applicable to the work by spanjool?  Basically he is saying that environment and other factors do affect SNP and STR mutation rates ( I wasn't aware of the latter).  It makes more sense to read this note from the bottom up.


They are applicable to any part of the chromosome where Polymerases are active - That seems to me to be the whole thing, autosomal and X or Y chromosomes. We do not seem to have a checking system for the hypervariable regions though. Genes like BRAC-1 and Brac-2 do not seem to check those regions for mutations and hence the mutations may not be corrected.

The same criteria for insertion of a guanine or any other base apply to the whole genome hence modifiers such as acetaldehyde would effect the hypervariable regions as well as the controlled/checked DNA segments. The study I am aware of shows that the hypervariable regions are effected by chemicals such as acetaldehyde but the differences in mutations rates compared with the control segments is not statistically significant - the researchers have stated that this may be the result of the technique they use.

Kind Regards
Neil McGregor
BDS, MDSc, PhD
Phone: 61 3 95721570
Email 1: neil.mcgregor1@bigpond.com
Email 2: binrm@bigpond.com
Email 3: NeilM@unimelb.edu.au

This message contains confidential information intended only for the use of the intended recipient(s) and may contain information that is privileged. If you are not the intended recipient, or the person responsible for delivering it to the intended recipient, you are hereby notified that reading, disseminating, distributing or copying this message is strictly prohibited.

-----Original Message-----
From: mcg11@frontiernet.net [mailto:mcg11@frontiernet.net]
Sent: Sunday, 24 June 2012 3:02 AM
To: Neil McGregor
Subject: Re: The randomness of the STR Mutational process

are your comments applicable to STR Y Mutations?  Or just autosomal?
----- Original Message -----
From: "Neil McGregor" <binrm@bigpond.com>
To: "Robert McGregor" <mcg11@frontiernet.net>
Cc: "Richard McGregor" <richardmcgregor1@yahoo.co.uk>, "peter lawrie" <peter.lawrie@glendiscovery.co.uk>
Sent: Wednesday, June 20, 2012 6:23:58 PM
Subject: The randomness of the STR Mutational process




Dear Bob,

 

Had a read of the article. It’s interesting to try to express mathematically what we see in real time mutations in genes. I will need some time to think about the relationships with what we see. Something not taken into account in this model though is what we see in malignant change.

If we place acetaldehyde into an epithelial cell culture and look at the mutations that are induced and then compare those with the mutations that occur naturally we see a significant difference in not only number but also location on the gene and its associated activator regions. The natural mutations seem to occur more frequently within the hyper variable regions whilst the mutations induced by acetaldehyde seem to occur more frequently within the exon/intron areas which are far more crucial to the gene function. What is important is that the chemical acetaldehyde interferes with Guanine use and insertion into the DNA so it must therefore be influencing one of the DNA polymerases. What seems to happen is that Guanine is substituted for Adenine more frequently. What this in effect does in produce mutations of certain types in specified areas of the DNA.

I f we look at the mutations induced by smoke v acetaldehyde v actinic radiation v other carcinogens we see different and identifiable patterns of mutations – these are NOT RANDOM.

Environmental factors, such as smoke or sunlight exposure, and dietary factors, such as alcohol or fermented vegetable consumption, soy beans as a major dietary source of carbohydrate, etc will provide an influence upon the mutations rate within a community and whilst they are not bottle neck producers as indicated in the discussion of disease, climate change, etc they are highly important effectors of the mutation rates within a given community. Simple examples of this selectivity can be seen in the Chinese v the Celts v the Germanic races v Africans, where dietary factors have induced significant changes in genes expression. In the Chinese its genes like ALDH2 (seems to have been induced as dietary Soy inhibits the enzyme), in the Europeans lactase deficiency (milk consumptions over a life time v only the first few years of life) and COMT polymorphisms (adaption to cold as induces an increase in thermogenesis), cold climate influences on sunlight exposure, vitamin D and white skin (fall in melanin (a major antioxidant)), etc.

If they are to devise a model then they need to take into account these types of influences into account. The models I have seen do not seem to do that.


 

Kind Regards

Neil McGregor

BDS, MDSc, PhD

Phone: 61 3 95721570

Email 1: neil.mcgregor1@bigpond.com

Email 2: binrm@bigpond.com

Email 3: NeilM@unimelb.edu.au

 
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A.D.
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« Reply #5 on: July 09, 2012, 01:22:28 PM »

 razyn. Thanks, I wouldn't have had a clue what spanjool was talking about  (my fault not his) but this is a really interesting and seemingly important subject.
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alan trowel hands.
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« Reply #6 on: July 09, 2012, 01:32:51 PM »

One factor that springs to mind to me is arsenical copper. 
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alan trowel hands.
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« Reply #7 on: July 09, 2012, 01:48:17 PM »

I am very familiar with the C14 curve and calibration.  I  take it the idea is that SNPs peak when C14 (and therefore background radiation) peaks?
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Jdean
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« Reply #8 on: July 09, 2012, 02:04:11 PM »

I am very familiar with the C14 curve and calibration.  I  take it the idea is that SNPs peak when C14 (and therefore background radiation) peaks?

If background radiation effects Y-DNA mutation rates then you would expect it to be observable in Cornish lines, I wonder if there are any reasonably long well researched Cornish families at FTDNA ?
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razyn
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« Reply #9 on: July 09, 2012, 03:58:50 PM »

One thing that interested me was the suggestion that solar activity might be less of a factor in the Δ14C spikes than a "nearby" supernova, which probably is to say one within our Milky Way galaxy.  The Crab Nebula is the remnant of a pretty recent one, observed in 1054; I don't know if that lines up with a Δ14C spike.  Anyway they are infrequent; and even one like 1987A (not in the Milky Way, but relatively nearby) caused "intense" radiation including neutrinos detected on earth, when the light-speed stuff began to arrive -- 160,000 years after the actual nova had happened.

http://en.wikipedia.org/wiki/List_of_supernovae

I don't think the Cornish mines would be analogous, since the background spikes would affect all life forms on the planet; but for all I know they might have some genetic effect observable in Cornwall.
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ironroad41
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« Reply #10 on: July 09, 2012, 06:27:30 PM »

I would also suggest that the recent "discovery" of the Higgs Gods particle plays a significant role also?
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