Launching the new Phase II A00 Research Project

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PostPosted: Thu May 30, 2013 2:53 pm
We recently saw this fascinating new paper appear:
> More Genomes From Denisova Cave Show Mixing of Early Human Groups
> Science 17 May 2013:
> Vol. 340 no. 6134 pp. 799DOI:10.1126/science.340.6134.799
Summary: Researchers have analyzed three fossil samples from Denisova Cave using a powerful new method that reveals ancient genomes in brilliant detail. One sample, a Neandertal toe bone, has yielded a nearly complete, high-coverage genome of our closest cousins, reported paleogeneticist Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, at The Biology of Genomes meeting last week. The analyses paint a complex picture of mingling among ancient human groups, and the data suggest inbreeding in Neandertals, a large Denisovan population, and mixing between Denisovans and an even earlier mystery species.


What exciting stuff!

Describing the way the different early humans are related, "It's more a network than a tree," Carlos Lalueza-Fox (a well known paleogeneticist who has worked on Neandertals) is quoted as saying.

It may become widely recognized and accepted that there has been repeated interbreeding between different varieties of humans, over many stages of our evolution within Africa, and this may prove to be the location where it happened most recently. Chris Stringer suggests as much in his 2012 book, Lone Survivors: How We Came to Be the Only Humans on Earth.

There's no need to artificially and rigidly define one of the diverse groups within Africa as the only "modern humans" and another one as archaic; in all likelihood, ancestral human populations have been alternating between genetic isolation and contact all along, with a variety of different populations contributing to our current genomes.

John Hawks very aptly commented,
> These were not isolated groups of ancient people, and some of them were more similar to living people than others. It is just wonderful to have more and more DNA coming out -- although that makes it hard to think we won't learn something new from high-coverage data that will require us to re-run various comparisons. That's the cost of discovery!

Yes! Wonderful data is coming from all over. I recently discovered that one of the new Phase III 1000 Genomes samples from the Gambia belongs to A0a1*, and is negative for all the known downstream SNPs defining A0a1a or A0a1b. It's only the second A0 we've found all in the 1K Genomes data. The Gambia is much further west than any A0 known until now.

Thanks to Greg Magoon for the excellent spreadsheets that make these analyses possible. Using them, I've been able to identify over 1500 SNPs that separate our two A0 samples from all the others. A similar number of SNPs are derived only in the A1a clade, the third oldest branch on the tree. Someday higher coverage data will become available, allowing more accurate estimates of the time depth of each of these branches.

But zero A00, two A0, and three A1a samples are very little to work with; to come up with really new data and discoveries, we need to do more sampling in Africa, our homeland and the hotbed of human diversity, and test these samples with up-to-date methods.

Therefore, a major phase II of citizen science research on haplogroup A00 is in the works. We plan to collect hundreds of new samples, both in the regions where A00 has been found, and in other promising areas, to get a better picture of where A00 is distributed. These samples may also provide data for other haplogroups, and for those who seek to connect their families' lineages back to Africa, depending on the kinds of support we're offered.

My main partner in this project is Matthew Fomine Forka Leypey, who collected the original Nkongho-Mbo A00 samples from his own people, along with over 2000 other samples from many peoples in Cameroon, an extremely diverse country. Stan Pietrzak is a steadfast supporter of this research, as always, and with Stan I'm exploring ways to contribute to the health, education, etc., of people in the villages where A00 is most often found, who have many urgent needs.

Matthew has shared his own private data set with me, which shows that no less than 30 members of A00 can already be identified, not only among the Mbo, but also in other ethnic groups in different regions of Cameroon. There are a few A0 as well, in addition to plenty belonging to haplogroups B, R1b, J, and of course E clades.

He's ready to head out to the field, to the forest villages in the mountains and lowlands, and once again gather samples from unsampled peoples and regions, including Pygmies; there were two A00 among the Pygmy samples Matthew has already collected (he doesn't now have access to the samples, only the data from a few STRs and SNPs).

In our project, we hope to return the test results to any DNA donors who are interested, which will be a new approach not usually taken in population genetics. If they are open to it, we may be able to allow genetic genealogists who match them, such as African-Americans, to make contact with them. Another possibility is to ask members of well-known, prominent patrilineages, of chiefs and traditional ritual leaders, to donate samples and allow their genealogies to be linked to the data, so that the oral or documented histories of their origins and migrations can contribute to our knowledge of A00 and other clades.

The only thing we need now, to enable us to move ahead, is financial support. We're going to be needing serious funding to do this. In addition to the costs of testing so many samples, there are expenses involved in fieldwork, even though Matthew isn't asking to be compensated for his time.

With luck, crowdfunding will be successful, since we don't fit into any of the typical categories that grantmakers deal with. But if anyone knows of a grant we could realistically apply for, please let me know.

The website that Andy Grierson and friends are using to raise the funds for their R1b research isn't available to us, since it was only possible via Andy's connections with the U. of Sheffield. Matthew is "ABD" at the U. of Yaounde 1, in Cameroon, but this research isn't part of his doctoral program. Thus we would need some institutional backing, or at least a non-profit organization to apply for grants.

I'm now calling for anyone who'd consider donating to please get in touch. I'd also appreciate any leads to find the best crowdfunding website to use. The three I've found for scientific research: Petridish, Microryza, and Iamscientist, don't look like they'd work for us. The first two require definite institutional backing, Petridish isn't taking any more projects right now, and the third has an expired security certificate, so I don't know if it's really functional. Should we try Kickstarter?

We're also examining the possibilities for testing by various labs. The first stage would be a simple screening for A00. This might be done at a lab where it will be most economical. After that we could send selected samples to Thomas Krahn for more in-depth testing. Not only that, but doing a full Y chromosome sequence, or even a full genome test, on at least one of the A00 samples, would be ideal! But it all depends on how much support we receive.

I'll be glad to hear from anyone and everyone who has helpful ideas and concrete support to contribute, either here, by email, or on Facebook, etc.

Bonnie Schrack

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Joined: Wed Mar 14, 2012 2:16 pm
PostPosted: Thu May 30, 2013 3:20 pm
Rootsy wrote:But if anyone knows of a grant we could realistically apply for, please let me know.

You could try the Scientific Grants Program of the Genographic Project:

http://blogs.discovermagazine.com/gnxp/ ... s-program/
https://genographic.nationalgeographic. ... ic-grants/
https://genographic.nationalgeographic. ... s_0912.pdf
---
The Genographic Scientific Grants Program awards grants on a rolling basis for projects that focus on studying the history of the human species utilizing innovative anthropological genetic tools. The varietyof projects supported by the Genographic Scientific grants will aim to construct our ancient migratory and demographic history while developing a better understanding the phylogeographic structure of world populations. Sample questions may include the origin and spread of the Indo-European-languages; genetic insights into Papua New Guinea's high linguistic diversity; the number and routes of migrations out of Africa; the origin of the Inca, or the genetic impact of the spread of maize agriculture in the Americas.
---
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Posts: 102
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PostPosted: Thu May 30, 2013 4:01 pm
lgmayka wrote:
Rootsy wrote:But if anyone knows of a grant we could realistically apply for, please let me know.

You could try the Scientific Grants Program of the Genographic Project:


Yes, thanks for your suggestion. I had identified that as one of the very few places that we might have a fair chance of winning a grant.

It has been suggested by some that these grants are primarily to fund Geno 2.0 tests by scientific researchers. But I hope they'll have a somewhat broader scope than that.

Bonnie

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MtDNA:
T2
PostPosted: Mon Jun 03, 2013 6:28 am
On the old dna-forums, I think we donated for DNA research through the Rockethub:
http://www.rockethub.com/projects/3709-ancient-roman-dna-project

However, haven't heard of any results or publications on Ancient Roman DNA yet.

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PostPosted: Thu Jul 25, 2013 6:56 am
Y-DNA A00 Fundraising Effort

GTC wrote:What are the goals of this project?

"Our research forms a part of the wider, global human project to understand the family tree that connects us all, both on a large scale and in detail. In 2012, we found a branch on the human Y-chromosome phylogenetic tree, haplogroup A00, that's far older than any other branch previously known, having its origins at the dawn of the human species' emergence. The only peoples on earth it's known to exist among are a few African-Americans, and Cameroonians of certain ethnic groups.

This research will begin to give us a picture of its true distribution and history. By collecting samples from a diverse range of ethnic groups in Cameroon, starting with those where A00 is known to occur, we hope to map it, and by analyzing the patterns of relationship between different A00 lineages, and the complex histories of these peoples, with their widely varying social structures and ecological adaptations, we hope to understand much more about A00's place in human history."

https://www.microryza.com/projects/y...f-the-homeland -

http://microryza.com/projects/y-dna-a00 ... e-homeland

Congratulations!

Posts: 77
Joined: Sat Dec 01, 2012 12:40 am

MtDNA:
T2
PostPosted: Mon Oct 14, 2013 11:13 am
The A00 Project has successfully reached the amount needed for sample collection in Cameroon, however more is required for testing them.

https://www.microryza.com/projects/which-of-cameroon-s-peoples-have-members-of-haplogroup-a00

Posts: 77
Joined: Sat Dec 01, 2012 12:40 am

MtDNA:
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PostPosted: Sat Nov 02, 2013 12:51 am
Come on, guys, with Mycroryza it is all or nothing. If the A00 project does not reach $8000 in five days, all the efforts go for nothing.
They need about $2000 more.

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