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  • Sonia
    replied
    Gram's ABD2.5 & CODIS

    Greetings everyone!
    Today I unpacked 15 of my 87 boxes at school Anyway, I've been thinking about Gram's CODIS results from DNAFP>DNA Tribes for about 3 weeks. Very curious stuff. Anyway, Gram is the least admixed of us Heinz 57 varieties in the family with her 2004 ABD 2.5 test indicating 82% Sub-Saharan African and 18% European. Her response then (at 99 you can say anything you want): "I don't care what any test says, I do have Indian in me and I don't have White in me." Anyway, she's been game for collecting her samples so we have them in the future and I thought we might get some interesting results from the CODIS Markers, but now I think that her admixture might still be too great to give us anything definitive. So, I'd keep this in mind if you're a well-admixed person. While the report gives her Top 20 Matches in each category, I'll just give the top 5. When you look at the numbers and compare them to those that people post on Charles Kercher's Log, you'll see what I mean about the results being far from informative, unless by Indian she means India Indian, but then again we've had that weird talk of SC Blackfoot (S: "They live in the Northern midwest & Canada, Gram." G: Wherever they are, my mother had Indian relatives in North Carolina." Over the past 10 years of online searching, I've discovered connections with 4 distant relatives, all who have heard the NC Indian connection (only Gram has the Blackfoot thing, but I've heard it from other South Carolinians). She also remembers being 3 or 4 when her mother died and an old Indian woman stayed with them. So, no DNA evidence, and she's the last of her line. Autosomal testing of nieces/nephews would throw in their other parents' DNA history.

    Part B Native Pop. Match from "338 Native Pops that have experienced minimal movement and admixture in modern history" and Part C Global Pop. Match from "511 global pops, including native peoples as well as Diaspora groups that have expanded from their homelands and sometimes admixed with others in recent history" were both the same:
    Upper Caste (Andhra Pradesh, India) - 49.8
    Lower Middle Caste (Andhra Pradesh, India) - 38.4
    Upper Middle Caste (Andhra Pradesh, India) - 37.2
    Mongol (Ximeng, Inner Mongolia) - 17.1
    Chueta (Spain) - 10.8
    And it goes down from there. The only African match was #18 in Part B of El-Minia, Egypt at 2.6 which was #19 in Part C.

    Part D World Region Matches "These regions are the product of long term patterns of interactions between peoples within major geographic and cultural zones over hundreds and often thousands of years." Really "weak" numbers:
    Sub-Saharan African - 0.4
    North African - 0.3
    Arabian - 0.1
    Tibetan - looks to be about 0.09
    Asia Minor - looks to be about 0.06
    Mestizo - about 0.05
    and they go way down from there.

    Any ideas?

    My thoughts - contamination? too much admixture? lab error? My advice - absolutely preserve the DNA, take the tests, but realize that with small sample sizes in the databases we won't know a lot for awhile. My next step is to order a kit for Gram from a company that stores DNA. That way I know I'll have a sample to test against these results in the future. (No, I haven't heard back from the company when I queried about whether they'd seen any other really weak results or whether they thought contamination could be a possibility.)

    I'm still working on understanding the Omnipop thingy, but the results do change significantly when I put both strands in and differ from when I put each strand in separately.

    Sonia

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  • GregKiroKH
    replied
    Originally posted by clarkedenise
    Thanks Dra. Ana,
    I research further the Codis testing.
    Denise
    I do not know why Asian DNA seems to replace Native American DNA for some people. I think it has to do with migration patterns.

    The AncestryByDNA 2.5 test will not allow customers to investigate each marker. This is a little frustrating. Still, they did a good job finding European markers.

    The Codis are well known. They have been used for years. So, one day, I would like to know my results because of the information available to the public.

    I think the commercial market has limited scientific reasoning. Still, it is interesting. So, I still look for good articles too.

    Leave a comment:


  • clarkedenise
    replied
    Codis Tests

    Thanks Dra. Ana,
    I research further the Codis testing.
    Denise

    Leave a comment:


  • casadecoqui
    replied
    The best explanation for the CODIS markers is on the website by DNA Fingerprint which offers the test. They also have samples of the reports which they send to their clients. It is the the new company located in Germany which merged with FTDNA. A new state of the art facility is being built in Houston to provide all their specialty tests stateside and will have a "super duper DNA sequencer".

    DNA Fingerprint

    It is true that it is difficult to tell whether the frequency of specific AIMs [Allele Informative Markers] is due to Native American or East Asian ancestry. This is obviously so because they share ancient ancestral roots. Haplogroups A, B, C, D and Native American Haplogroup X are derived from those groups which migrated from around the Mongolian Lake Biakal area and crossed the Bering Strait to North America.

    The Biogeographical test (BGA) is still, at best, imperfect since although it should pick up traces up to 5 generations back, it falls short of that.

    For instance, I am admixed individual. (Duh) However, on the 2.0 test, I was 76% European and 24% East Asian and 0% NA, 0% SA. My maternal grandfather and grandmother are Native American Haplogroup C. I have others as well. There are no documented Asians in my lines literally as far back as the colonization. My ancestors have been on the island since before the Indians guided the lost Columbus to their land. That 24% is undoubtedly from my Taíno ancestry and not East Asian.

    On the other hand, my maternal 4th great grandmother and about 10 other couples on both paternal and maternal side were slaves. So, the BGA as it is now obviously does not do well at providing AIMs which can significantly and accurately determine ancestry in admixed peoples ... or others for that matter unless they are overwhelmingly European.

    The CODIS markers on the other hand are used forensically and are biparental, ie. one would be sure to pick up DNA obtained through recombination which has occurred generation after generation. This DNA information is inherited from the rest of your ancestors. It provides more ancestral data than if you just were to test the yDNA or solely the mtDNA from your 2 immediate ancestors, your parents. The information from the CODIS markers would help better define your probable ancient ancestral associations by comparing the results to a CODIS database.

    Originally posted by clarkedenise
    Dear Dra. Ana & Greg,
    I also recently received my autosomal test results this month. I had the Ancestry By DNA 2.5. Here are my results: 56% Sub-Saharan African, 33% European, 11% East Asian, 0% Native American. East Asian was surprising, however; I'm told that Native Ancestry sometimes will show up as East Asian. Should I also consider doing a Codis test and what should I expect to learn from this test?
    Denise

    Leave a comment:


  • clarkedenise
    replied
    Autosomal Test Results

    Dear Dra. Ana & Greg,
    I also recently received my autosomal test results this month. I had the Ancestry By DNA 2.5. Here are my results: 56% Sub-Saharan African, 33% European, 11% East Asian, 0% Native American. East Asian was surprising, however; I'm told that Native Ancestry sometimes will show up as East Asian. Should I also consider doing a Codis test and what should I expect to learn from this test?
    Denise

    Leave a comment:


  • casadecoqui
    replied
    Greg and all members:

    I'm always looking for any new articles. If I can get them, I will post them here!

    I've also done the DNAPrint 2.0 and 2.5. I am waiting for a kit to get my CODIS markers tested.

    For those of you who don't know what these autosomal biparental markers are, they are the markers on all the rest of our chromosomes. These have bits of information inherited from all of our ancestors, both paternal and maternal.

    They include:

    CSF1PO
    D3S1358
    D5S818
    D7S820
    D8S1179
    D13S317
    D16S539
    D18S51
    D21S11
    FGA (=FIBRA)
    Penta D
    Penta E
    TH01
    TPOX
    vWA
    D2S1338
    D19S433
    F13A01
    F13B
    FESFPS
    LPL
    Penta B
    Penta C
    SE33 (=ACTBP2)

    The results are compared to a database of African, East Asian, Native American and European populations to help determine with which group one has the greatest affinity.

    BTW, in case you were not aware, we are the featured DNA Project of the week for ISOGG!

    Thank you all for participating.

    Originally posted by GregKiroKH
    Thanks for making it available, Ana. I think it is a nice article even thou it is from 1999. It is the same article. I had a copy on my key, and I read it this morning. I think I am excited about genetics again. Are there any newer articles to read concerning autosomes or human genetics?

    Leave a comment:


  • GregKiroKH
    replied
    Originally posted by casadecoqui
    Greg,

    What's the name of the article? Your link will only take people to the registration or splash page.

    Is it "A brief history of human autosomes" by D. Haig?
    I have access and attached a copy below.
    Thanks for making it available, Ana. I think it is a nice article even thou it is from 1999. It is the same article. I had a copy on my key, and I read it this morning. I think I am excited about genetics again. Are there any newer articles to read concerning autosomes or human genetics?

    Leave a comment:


  • casadecoqui
    replied
    Greg,

    What's the name of the article? Your link will only take people to the registration or splash page.

    Is it "A brief history of human autosomes" by D. Haig?
    I have access and attached a copy below.


    Originally posted by GregKiroKH
    http://www.journals.royalsoc.ac.uk/m...b78qa6vedc.pdf

    I was at school looking for interesting articles covering autosomes. This was an interesting article, but I could not get it from home because I do not have a password.
    Attached Files
    Last edited by casadecoqui; 25 August 2006, 07:30 PM.

    Leave a comment:


  • GregKiroKH
    replied
    http://www.journals.royalsoc.ac.uk/m...b78qa6vedc.pdf

    I was at school looking for interesting articles covering autosomes. This was an interesting article, but I could not get it from home because I do not have a password.

    Leave a comment:


  • Sasa
    replied
    Africans in the Americas

    BLACK CIVILIZATIONS OF ANCIENT AMERICA (MUU-LAN), MEXICO (XI)
    (beautiful photos of artifacts at website)

    http://www.raceandhistory.com/histor...entamerica.htm

    Gigantic stone head of Negritic African
    during the Olmec (Xi) Civilization

    By Paul Barton
    Negritic African The earliest people in the Americas were people of the Negritic African race, who entered the Americas perhaps as early as 100,000 years ago, by way of the bering straight and about thirty thousand years ago in a worldwide maritime undertaking that included journeys from the then wet and lake filled Sahara towards the Indian Ocean and the Pacific, and from West Africa across the Atlantic Ocean towards the Americas.

    According to the Gladwin Thesis, this ancient journey occurred, particularly about 75,000 years ago and included Black Pygmies, Black Negritic peoples and Black Australoids similar to the Aboriginal Black people of Australia and parts of Asia, including India.

    Ancient African terracotta portraits 1000 B.C. to 500 B.C.
    African terracotta Recent discoveries in the field of linguistics and other methods have shown without a doubt, that the ancient Olmecs of Mexico, known as the Xi People, came originally from West Africa and were of the Mende African ethnic stock. According to Clyde A. Winters and other writers (see Clyde A. Winters website), the Mende script was discovered on some of the ancient Olmec monuments of Mexico and were found to be identical to the very same script used by the Mende people of West Africa. Although the carbon fourteen testing date for the presence of the Black Olmecs or Xi People is about 1500 B.C., journies to the Mexico and the Southern United States may have come from West Africa much earlier, particularly around five thousand years before Christ. That conclusion is based on the finding of an African native cotton that was discovered in North America. It's only possible manner of arriving where it was found had to have been through human hands. At that period in West African history and even before, civilization was in full bloom in the Western Sahara in what is today Mauritania. One of Africa's earliest civilizations, the Zingh Empire, existed and may have lived in what was a lake filled, wet and fertile Sahara, where ships criss-crossed from place to place.

    ANCIENT AFRICAN KINGDOMS PRODUCED
    OLMEC TYPE CULTURES

    The ancient kingdoms of West Africa which occupied the Coastal forest belt from Cameroon to Guinea had trading relationships with other Africans dating back to prehistoric times. However, by 1500 B.C., these ancient kingdoms not only traded along the Ivory Coast, but with the Phoenicians and other peoples. They expanded their trade to the Americas, where the evidence for an ancient African presence is overwhelming. The kingdoms which came to be known by Arabs and Europeans during the Middle Ages were already well established when much of Western Europe was still inhabited by Celtic tribes. By the 5th Century B.C., the Phoenicians were running comercial ships to several West African kingdoms. During that period, iron had been in use for about one thousand years and terracotta art was being produced at a great level of craftsmanship. Stone was also being carved with naturalistic perfection and later, bronze was being used to make various tools and instruments, as well as beautifully naturalistic works of art.

    The ancient West African coastal and interior Kingdoms occupied an area that is now covered with dense vegetation but may have been cleared about three to four thousand years ago. This includes the regions from the coasts of West Africa to the South, all the way inland to the Sahara. A number of large kingdoms and empires existed in that area. According to Blisshords Communications, one of the oldest empires and civilizions on earth existed just north of the coastal regions into what is today Mauritania. It was called the Zingh Empire and was highly advanced. In fact, they were the first to use the red, black and green African flag and to plant it throughout their territory all over Africa and the world.........CONTINUED

    http://www.raceandhistory.com/histor...entamerica.htm

    Leave a comment:


  • casadecoqui
    replied
    An Ancient Link to Africa Lives on in Bay of Bengal

    ************************************************** ******
    Article Posted by Sasa

    Forum Admin Note: (moved to this thread, 07-04-2006)

    ************************************************** ******

    An Ancient Link to Africa Lives on in Bay of Bengal

    Posted: Tuesday, December 24, 2002

    Author: Nicholas Wade
    Filed: 12/11/2002
    Source: The New York Times
    http://www.nytimes.com/2002/12/10/science/10ISLA.html

    Inhabitants of the Andaman Islands, a remote archipelago east of India, are direct descendants of the first modern humans to have inhabited Asia, geneticists conclude in a new study.

    But the islanders lack a distinctive genetic feature found among Australian aborigines, another early group to leave Africa, suggesting they were part of a separate exodus.

    The Andaman Islanders are "arguably the most enigmatic people on our planet," a team of geneticists led by Dr. Erika Hagelberg of the University of Oslo write in the journal Current Biology.

    Their physical features — short stature, dark skin, peppercorn hair and large buttocks — are characteristic of African Pygmies. "They look like they belong in Africa, but here they are sitting in this island chain in the middle of the Indian Ocean," said Dr. Peter Underhill of Stanford University, a co-author of the new report.

    Adding to the puzzle is that their language, according to Joseph Greenberg, who, before his death in 2001, classified the world's languages, belongs to a family that includes those of Tasmania, Papua New Guinea and Melanesia.

    Dr. Hagelberg has undertaken the first genetic analysis of the Andamanese with the help of two Indian colleagues who took blood samples — the islands belong to India — and by analyzing hair gathered almost a century ago by a British anthropologist, Alfred Radcliffe-Brown. The islands were isolated from the outside world until the British set up a penal colony there after the Indian mutiny of 1857.

    Only four of the dozen tribes that once inhabited the island survive, with a total population of about 500 people. These include the Jarawa, who still live in the forest, and the Onge, who have been settled by the Indian government.

    Genetic analysis of mitochondrial DNA, a genetic element passed down only through women, shows that the Onge and Jarawa people belong to a lineage, known as M, that is common throughout Asia, the geneticists say. This establishes them as Asians, not Africans, among whom a different mitochondrial lineage, called L, is dominant.

    The geneticists then looked at the Y chromosome, which is passed down only through men and often gives a more detailed picture of genetic history than the mitochondrial DNA. The Onge and Jarawa men turned out to carry a special change or mutation in the DNA of their Y chromosome that is thought to be indicative of the Paleolithic population of Asia, the hunters and gatherers who preceded the first human settlements.

    The mutation, known as Marker 174, occurs among ethnic groups at the periphery of Asia who avoided being swamped by the populations that spread after the agricultural revolution that occurred about 8,000 years ago. It is found in many Japanese, in the Tibetans of the Himalayas and among isolated people of Southeast Asia, like the Hmong.

    The discovery of Marker 174 among the Andamanese suggests that they too are part of this relict Paleolithic population, descended from the first modern humans to leave Africa.

    Dr. Underhill, an expert on the genetic history of the Y chromosome, said the Paleolithic population of Asia might well have looked as African as the Onge and Jarawa do now, and that people with the appearance of present-day Asians might have emerged only later. It is also possible, he said, that their resemblance to African Pygmies is a human adaptation to living in forests that the two populations developed independently.

    A finding of particular interest is that the Andamanese do not carry another Y chromosome signature, known as Marker RPS4Y, that is common among Australian aborigines.

    This suggests that there were at least two separate emigrations of modern humans from Africa, Dr. Underhill said. Both probably left northeast Africa by boat 40,000 or 50,000 years ago and pushed slowly along the coastlines of the Arabian Peninsula and India. No archaeological record of these epic journeys has been found, perhaps because the world's oceans were 120 meters lower during the last ice age and the evidence of early human passage is under water.

    One group of emigrants that acquired the Marker 174 mutation reached Southeast Asia, including the Andaman islands, and then moved inland and north to Japan, in Dr. Underhill's reconstruction. A second group, carrying the Marker RPS4Y, took a different fork in Southeast Asia, continuing south toward Australia.

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  • casadecoqui
    replied
    News Article

    News Article on Yahoo - soon to be published in Nature Magazine

    Roots of Human Family Tree are shallow

    Leave a comment:


  • casadecoqui
    replied
    Thanks, Greg.

    For those that don't know of Dr. Vincent Macaulay's work, here is his URL:

    Vincent Macaulay's Home page

    Originally posted by GregKiroKH
    I found a link to the article at Vincent Macaulay's website. He also has links to some of his recent research papers.

    Leave a comment:


  • GregKiroKH
    replied
    Originally posted by lee1906
    Dr. Ana,

    I can send you a pdf copy of this article. Just send me an email.

    Hoyte
    I found a link to the article at Vincent Macaulay's website. He also has links to some of his recent research papers.

    Leave a comment:


  • casadecoqui
    replied
    Thanks, "cuz"!

    Originally posted by lee1906
    Dr. Ana,

    I can send you a pdf copy of this article. Just send me an email.

    Hoyte

    Leave a comment:

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