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 Post subject: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 4:38 pm 
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I asked this regarding the dating of X2a in one of Simon Southerton's threads, but never got an answer. If Simon or The Dude or any other DNA knowledgeable person is paying attention I hope I could hear from them on this. This is a bit of a long story, so I'll try to just hit the highlights.

I have a good friend in the ward that that maintains that X2a 'could be semitic' since X2 is largely only found in Druze and Native Americans. We've gone back and forth a bit on this.

My position has been that I didn't think the timing could support X2a being Lehite. He originally argued for a founder/bottleneck effect that could make the timing much shorter. I found a few papers like
Fugundes et al. (2008) Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas, AJHG, 82, 583-592
and a few others (A 2008 Science papers and some others that I can't remember. I let him take them). All of the papers I came up with had minimum coalescence dates of >11,000 YBP - even taking into account founders/bottlenecks.

His position is now that the dating of the papers I found is likely using much too slow mutation rates and sent me the following paper:
Parsons et al. (1997) A high observed substitution rate in the human mitochondrial DNA control region, Nature Genetics, 15, 363-368
The experimentally measured rate in the Parsons paper would result in a timing of X2a coalescence of ~2300 +/- 900 YBP.

There are 355 citations for Parsons et al. according to Google Scholar. I can't believe that all the papers I found (publication dates between 2003 - 2010) were ignorant of Parsons work. Also, if I am not mistaken, the proponents of European-origin Clovis, who would have incentive to embrace the shorter time scales, haven't seemed to latch on to the shorter times to make their case.

My friend is an analytical chemist that does research on proteins, so he is a big step closer to the field than I am. So, if any DNA experts are paying attention, I would much appreciate an explanation of X2a dating and what a rigorous range of X2a coalescence dates could be.

Lastly, I tried to find the Pundit discussion between The Dude and David Stewart, but I couldn't find it - has it disappeared into the ether with so much of the FAIR discussion board history?


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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 5:27 pm 
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Hi NorthboundZax

I have a post on my blog that talks about the X lineage. http://simonsoutherton.blogspot.com.au/2011/12/origin-of-x-lineage.html.

At the bottom of my blog I point readers to a critique of Meldrum's X lineage claims. Make sure to read it because it is written by scientists whose work has been distorted by Meldrum. They are furious.

Cheers
Simon

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 5:33 pm 
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Quote:
I have a good friend in the ward that that maintains that X2a 'could be semitic' since X2 is largely only found in Druze and Native Americans


See the Skeptical Inquirer article

Haplogroup X is found throughout the Near East, western Eurasia, and northern Africa, and it is not unique to (nor especially common in) Israelite or Jewish populations (Reidla et al. 2003; Behar et al. 2004).

the forms of haplogroup X found in the Galilee Druze (and elsewhere in the Near East) are not closely related to the particular form of haplogroup X found in Native Americans.

The Hopewell and other Native American populations exhibit sub-haplogroup X2a, which is different from the subhaplogroups present in the Galilee Druze (subhaplogroups X2*, X2b, X2e, X2f) or other Middle Eastern populations

Quote:
His position is now that the dating of the papers I found is likely using much too slow mutation rates


From the Skeptical Inquirer article

Meldrum does not rely on newer findings to argue that haplogroup X began to diversify and spread only two thousand years ago, as he claims, but rather on an old and unusually fast estimate of the mtDNA mutation rate (Parsons et al. 1997). Virtually all pedigree studies have found significantly lower mutation rates (Howell et al. 2003) than the one Meldrum uses, which suggests that haplogroup X began diversifying much earlier than he claims. Studies of the complete mitochondrial genome (rather than just the control region), using less controversial mutation rates for the mtDNA coding region, also suggest that haplogroup X began to diversify much earlier (~31,800 years ago; Soares et al. 2009).

Quote:
My friend is an analytical chemist that does research on proteins


Have him read these -

Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking When it comes to mtDNA, one should not use a sundial as a stopwatch.

Soares et al. 2009 We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.


Last edited by tapirrider on Sun Jun 10, 2012 5:58 pm, edited 1 time in total.

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 5:51 pm 
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You can trust anything written by people with a fascination for Tapirs.

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 6:49 pm 
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NorthboundZax wrote:
Lastly, I tried to find the Pundit discussion between The Dude and David Stewart, but I couldn't find it - has it disappeared into the ether with so much of the FAIR discussion board history?


Yep, it's gone. IIRC, we didn't really get into mtDNA because David's pseudoscientific façade was constructed from supposed links in Y chromosome analysis.

Don't get sucked into arguing about absolute dates and mutation rates. You can rule out the possibilities your friend is pushing by understanding the correct relationship between the different X lineage sub clades, as Simon points out on his blog. That's all you need.

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 8:43 pm 
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Thanks, guys! That is a lot of help. I should have realized this was Meldrum-driven, but I gave him more credit than that. As a side note, if Meldrum is winning PhD chemist seminary teachers over FARMS, it is no wonder FARMS would be doing a full court press against him. They used to only compete with Sunstone for that demographic.

The Dude wrote:
Yep, it's gone. IIRC, we didn't really get into mtDNA because David's pseudoscientific façade was constructed from supposed links in Y chromosome analysis.


That's too bad. Both that and your LDA spiritual experience threads are real losses. Should I be expecting my friend to throw Y chromosome pseudoscience my way at some point?

Quote:
Don't get sucked into arguing about absolute dates and mutation rates. You can rule out the possibilities your friend is pushing by understanding the correct relationship between the different X lineage sub clades, as Simon points out on his blog. That's all you need.


I had already laid out the difference in sub clades, but to me the difference between X2a and X2*/b/g/etc is most apparent by noting time of divergence. So could you flesh out the real importance of the distinction independent of timing? For example, suppose we were determined to stick with the superfast Parsons mutation rate, am I hearing that one couldn't get X2a out of one of the middle East X2s via founder effect?


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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Sun Jun 10, 2012 9:03 pm 
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NorthboundZax wrote:
That's too bad. Both that and your LDA spiritual experience threads are real losses.


Thanks man. Those were the days.

Quote:
I had already laid out the difference in sub clades, but to me the difference between X2a and X2*/b/g/etc is most apparent by noting time of divergence. So could you flesh out the real importance of the distinction independent of timing? For example, suppose we were determined to stick with the superfast Parsons mutation rate, am I hearing that one couldn't get X2a out of one of the middle East X2s via founder effect?


Outside of a tortured effort to make sense of the Book of Mormon, there's no justification for peeling off X2a and saying it had a special mutation rate. It's all or nothing. If you apply a superfast mutation rate to X2a then you have to apply it to everything. All of the sudden you are saying ALL the mtDNA groups came to the New World possibly as recently as 600BC. That can't be right, however, because archaeology shows that there were people established here way before then. And every apologist knows that Lehi's few people couldn't have expanded and supplanted the long established DNA groups in the entire hemisphere in a couple thousand years.

Focus on the relative time of divergence and imagine what it would look like if you compressed the whole timeline into the Book of Mormon period. Does that make sense with archaeology and geography? No it doesn't.

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Mon Jun 11, 2012 6:17 am 
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Simon Southerton wrote:
You can trust anything written by people with a fascination for Tapirs.


LOL

Hi Simon. I only ride the tapir to have fun with silly apologists. Horses are much more fascinating.


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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Mon Jun 11, 2012 6:22 am 
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tapirrider wrote:
Simon Southerton wrote:
You can trust anything written by people with a fascination for Tapirs.


LOL

Hi Simon. I only ride the tapir to have fun with silly apologists. Horses are much more fascinating.


And your feet don't drag on the ground so much. :wink:

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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Tue Jun 12, 2012 11:02 am 
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The Dude wrote:
Outside of a tortured effort to make sense of the Book of Mormon, there's no justification for peeling off X2a and saying it had a special mutation rate. It's all or nothing. If you apply a superfast mutation rate to X2a then you have to apply it to everything. All of the sudden you are saying ALL the mtDNA groups came to the New World possibly as recently as 600BC. That can't be right, however, because archaeology shows that there were people established here way before then. And every apologist knows that Lehi's few people couldn't have expanded and supplanted the long established DNA groups in the entire hemisphere in a couple thousand years.

Focus on the relative time of divergence and imagine what it would look like if you compressed the whole timeline into the Book of Mormon period. Does that make sense with archaeology and geography? No it doesn't.


Ah, OK I am with you now. If X2a were young, the Siberian migration would be just as young. That should be pretty golden.


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 Post subject: Re: timing of X2a clade - calling DNA experts
PostPosted: Tue Jun 12, 2012 5:42 pm 
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You all are equally blinded by your abject hatred of Mormonism and are clearly nothing but puppets of Doctor Scratch.

You are all the same person, and I'll let you guess who that is.

Cease your campaign of defamation against Daniel Peterson in this thread right away.

Your party is coming to an end very soon.

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