Announcement

Collapse
No announcement yet.

Articles and Interesting Links

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • casadecoqui
    replied
    Article on Y, X, autosomal and mtDNA in African Americans

    Hum Genet. 2007 Jan;120(5):713-22. Epub 2006 Sep 28.

    Elevated male European and female African contributions to the
    genomes of African American individuals.


    Lind JM, Hutcheson-Dilks HB, Williams SM, Moore JH, Essex M,
    Ruiz-Pesini E, Wallace DC, Tishkoff SA, O'Brien SJ, Smith MW.

    Laboratory of Genomic Diversity, NCI-Frederick, Frederick, MD, USA.

    The differential relative contribution of males and females from
    Africa and Europe to individual African American genomes is relevant
    to mapping genes utilizing admixture analysis. The assessment of
    ancestral population contributions to the four types of genomic DNA
    (autosomes, X and Y chromosomes, and mitochondrial) with their
    differing modes of inheritance is most easily addressed in males. A
    thorough evaluation of 93 African American males for 2,018 autosomal
    single nucleotide polymorphic (SNP) markers, 121 X chromosome SNPs, 10
    Y chromosome haplogroups specified by SNPs, and six haplogroup
    defining mtDNA SNPs is presented. A distinct lack of correlation
    observed between the X chromosome and the autosomal admixture
    fractions supports separate treatment of these chromosomes in
    admixture-based gene mapping applications. The European genetic
    contributions were highest (and African lowest) for the Y chromosome
    (28.46%), followed by the autosomes (19.99%), then the X chromosome
    (12.11%), and the mtDNA (8.51%). The relative order of admixture
    fractions in the genomic compartments validates previous studies that
    suggested sex-biased gene flow with elevated European male and African
    female contributions. There is a threefold higher European male
    contribution compared with European females (Y chromosome vs. mtDNA)
    to the genomes of African American individuals meaning that
    admixture-based gene discovery will have the most power for the
    autosomes and will be more limited for X chromosome analysis.

    PMID: 17006671 [PubMed - indexed for M ]

    Leave a comment:


  • Uncommontreasur
    replied
    Congratulations Dra. Ana

    Press Release:

    From: Fred Willard, Director of the Lost Colony Center for Science and Research, and Roberta Estes, Director of DNA Research for the Lost Colony Center for Science and Research

    Date: June 21, 2007

    It is our pleasure to announce the addition of Dr. Ana Oquendo Pabón, MD to the advisory board of the Lost Colony Center for Science and Research as our advisor for DNA and Historical Research. In addition to Dr. Oquendo Pabón’s private medical practice, she has developed a specialty in mitochondrial DNA.

    Her DNA and research interests include the Native Population of Puerto Rico as well as that of the United States and the African Diaspora.

    In 2003, as early genetic genealogy pioneers, she co-founded the Puerto Rican Geographical DNA project with her brother, Rev. Father Jose Antonio Oquendo Pabón, a humanities professor, island historian, genealogist, and researcher. Through the project and the collaboration of their members, they have successfully determined the ancestral haplotype of many of the oldest surnames on the island such as the Maldonado, the Rivera de Mathos, Ramírez de Arellano and others.

    From the outset, Dr. Oquendo Pabón vigorously encouraged mitochondrial DNA testing of DNA participants, corroborating the results of previous scientific studies which have shown the extremely high ancestral frequency of the purportedly extinct Native American/ Taíno people of Puerto Rico.

    Dr. Oquendo Pabón’s extensive knowledge of mitochondrial DNA, Native American DNA, genealogy and early historical documents is a welcome addition to the resources of the Lost Colony Center for Science and Research. She will be attending the Lost Colony Symposium on DNA and Recent Research on Sept. 7-9, 2007 at the Lost Colony Center in Washington, NC.

    Welcome, Dr. Oquendo Pabón!




    Barton DNA Project:

    http://www.bartondna.info/

    Leave a comment:


  • GregKiroKH2
    replied
    Thanks Ana, I think I have finally learned my lesson. Never turn in article the same day I write it. It might be dangerous to my mental health

    I will look forward to your E-mail. I know you are excited with the results. I remember there were at least two branches to the L1c1a tree, 93 and 44. I have 3843G not the 8087 for L1c1a. I wonder if that is important?

    Gregory

    Originally posted by casadecoqui
    I really was ROFL when I read this one, Greg. I haven't been able to log on to the forum since the new web site changes. What you say is certainly true. I find my old biology, biochemistry and genetics books from med school certainly are holding their own.

    Have finally gotten my MEGA results. I am now L1c1a. I'll send you an e-mail.

    Ana

    Leave a comment:


  • casadecoqui
    replied
    I really was ROFL when I read this one, Greg. I haven't been able to log on to the forum since the new web site changes. What you say is certainly true. I find my old biology, biochemistry and genetics books from med school certainly are holding their own.

    Have finally gotten my MEGA results. I am now L1c1a. I'll send you an e-mail.

    Ana

    Originally posted by GregKiroKH2
    I think I had a good dialogue with myself. I still could not find a good reference. My Biochem I lab class provided me more information than everything I read on a search engine search. I always thought experience was golden. Still, it was good old reasoning which won it for me.

    Leave a comment:


  • GregKiroKH2
    replied
    I think I had a good dialogue with myself. I still could not find a good reference. My Biochem I lab class provided me more information than everything I read on a search engine search. I always thought experience was golden. Still, it was good old reasoning which won it for me.

    Leave a comment:


  • GregKiroKH2
    replied
    You have a misconception, Greg. First, the fonts were wrong in your quote. It should read L1 (+3592 HpaI, -10806 HinfI), L2 (+3592 HpaI, -16390 HinfI), and L3 (-3592 HpaI). The "1" was a "+," and the "2" was a "-." Second, HpaI is a restriction enzyme. Strickly speaking a cut is not a mutation. Thirdly, these old journal articles do not include the DNA base. However, it is true that 3594 is seen with L3.

    HpaI, Restriction Endonucleases

    5' . . . GTT*AAC . . . 3'
    rCRS 3950 GGTCAACCAA

    Originally posted by GregKiroKH2
    L3 does not have the mutation 3592. The minus sign means that it was lost with the L3 people. This is why it is not seen much outside of Africa.
    Available Enzymes:

    AccIII => TCCGGA
    Acc651 => GGTACC
    AgeI => ACCGGT
    AluI => AGCT
    ApaI => GGGCCC
    BalI => TGGCCA
    BamHI => GGATCC
    BbuI => GCATGC
    BclI => TGATCA
    BglII => AGATCT
    BssHII => GCGCGC
    Bst981 => CTTAAG
    BstZI => CGGCCG
    CfoI => GCGC
    ClaI => ATCGAT
    Csp451 => TTCGAA
    DraI => TTTAAA
    Eco47III => ACGGCT
    Eco521 => CGGCCG
    EcoRI => GAATTC
    EcoRV => GATATC
    HaeII I=> GGCC
    HhaI => GCGC
    HindIII => AAGCTT
    HpaI => GTTAAC
    HpaII => CCGG
    KpnI => GGTACC
    MboI =>GATC
    MluI => ACGCGT
    MspI => CCGG
    NaeI => GCCGGC
    Nar => GGCGCC
    NcoI => CCATTGG
    NdeI => CATATG
    NgoMI => GCCGGC
    NheI => GCTAGC
    NotI => GCGGCCGC
    NruI => TCGCGA
    NsiI => ATGCAT
    PstI => CTGCAG
    PvuI => CGATCG
    RvuII => CAGCTG
    RsaI => GTAC
    SacI => GAGGCTC
    SacII => CCGCGG
    SalI => GTCGAC
    Sau3AI => GATC
    ScaI => ACTACT
    SfgI => GCGATCGC
    SmaI => CCCGGG
    SnaBI => TACGTA
    SpeI => ACTAGT
    SphI => GCATGC
    SspI => AATATT
    StuI => AGGCCT
    TaqI => TCGA
    Tru91 => TTAA
    VspI => ATAAT
    XbaI => TCTAGA
    XhoI => CTCGAG
    XmaI =>CCCGGG

    http://marycarol.hypermart.net/cgi-bin/4.pl

    Leave a comment:


  • GregKiroKH2
    replied
    L3 does not have the mutation 3592. The minus sign means that it was lost with the L3 people. This is why it is not seen much outside of Africa.

    Originally posted by GregKiroKH2
    What does it mean if a L has the 3594 mutation instead of the 3592 mutation?

    Leave a comment:


  • GregKiroKH2
    replied
    What is the Difference between 3594 L3 and 3592 L3?

    What does it mean if a L has the 3594 mutation instead of the 3592 mutation?

    We build on the phylogenetic analyses of European (Richards et al. 1998; Macaulay et al. 1999) and African (Rando et al. 1998) mtDNA, which combine HVS-I and RFLP information. According to the nomenclature of those analyses, human mtDNAs are divided into three supergroups—L1 (13592 HpaI, 210806 HinfI), L2 (13592 HpaI, 216390 HinfI), and L3 (23592 HpaI). L1 and L3 are further subdivided into haplogroups, which can be recognized by specific restriction sites (table 1).
    http://www.gene.com.br/ExamesGenetic...ilianmtDNA.pdf

    Leave a comment:


  • GregKiroKH2
    replied
    We were talking about the distribution of polymorphisms between different haplogroups. And the topic a Lorentzian and Gaussian waveshapes came up. Why do you think there are distributions of polymorphisms?

    Control region rates follow a negative binomial distribution (gamma distribution).
    Most sites -invariant
    Few sites -fast

    High α(low variation)
    Low α(high variation)

    The SHAPE of the curve (α) is inversely related to the amount of heterogeneity
    Yang, 1996

    Meyer and von Haeseler (2003) Mol. Biol Evol. Analyzed the 53 mtGenomes from Ingman et al. (2000).
    http://www.cstl.nist.gov/biotech/str...dingregion.pdf

    Leave a comment:


  • casadecoqui
    replied
    Hidden African Ancestors

    Hidden African Ancestors: Hidden secrets of your ancestors

    Peter de Knijff1

    1Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University, Medical Center, P O Box 9600, 2300 RC Leiden, The Netherlands

    Correspondence: Peter de Knijff, Tel: +31 71 526 9537; Fax: +31 71 526 8278; E-mail: [email protected]

    Genealogy is no longer simply a matter of pen, paper, and patience. It seems that modern genealogical reconstruction is not complete without genetic confirmation by means of Y-chromosome genotyping. As usual, when there is a demand, commercial enterprises pop up like autumnal mushrooms. A simple Google search with genealogy+y+DNA results in approximately 468 000 hits. Many of these sites are surname-specific projects or internet companies offering commercial genotype services. What these companies offer is what I call a blindfold scenario: a male with surname X has his Y-profile typed and compared to all other types in the companies' database in the hope of finding a (near) match to someone else in the database irrespective of its surname. The error-prone nature of such a process is perfectly illustrated by the link by Oxford Ancestors of one of their clients to Genghis Khan.1 Only rarely genealogists adopt the much more reliable open-eyed hypothesis driven kind of request: a genealogist has reconstructed a certain pedigree and either wants to have this pedigree confirmed or needs a genetic 'link' between branches of the pedigree which cannot be linked otherwise. This pedigree-based design was also used to obtain the first mutation rates of Y-STRs2 and the reconstruction of the pedigree of Thomas Jefferson.3

    In most Western societies surnames are co-transmitted with Y-chromosomes. As a consequence, surname and Y-chromosome reflect the same patrilineal ancestry. Generally speaking, the rarer a surname, the better its transmission over time reflects that of a particular Y-chromosome.4 It has even been shown that in the ideal case population substructure can be inferred only on the basis of detailed surname analyses.5 Although this might be true in general, in isolated cases false paternity or in vitro fertilization by means of anonymous sperm donors disrupts the link between a particular surname and its corresponding Y-chromosomal genotype. Of course, also a perfectly legal marriage can introduce 'exotic' Y-chromosomes into a pedigree. When this happened in the past, and is not adequately documented, one could learn something quite unexpected about one's ancestors. This is exactly what was described in the recent issue of this journal.6

    King et al, much to their own surprise, discovered a single male carrying a classical African Y-chromosome type, called haplogroup A1, among a set of 421 males who were analyzed as part of an ongoing large British surname study. The surname of this male matched to another 121 individuals in the public record, predominantly in east Yorkshire. From these, 18 apparently unrelated males were relocated and genotyped. Of these, six more males also carried the same African A1 Y-chromosome. Genealogical research allowed them to be connectedto two pedigrees going back to 1788 AD and 1789 AD. These two pedigrees could not be connected, but a detailed Y-chromosome study strongly suggests that originally they must share a single common male ancestor. As such, the presence of African Y-chromosomes among Western European populations is not without precedent. At least for Britain, the presence of Africans has been reported since 200 AD (see King et al.6). However, what is surprising is the exact type of African Y-chromosome. In Africa itself three major Y-haplogroups are most frequently observed (A, B, and E) with frequencies of approximately 7.3, 11, and 69%, respectively. The frequency of haplogroup A1 is only about 1% in Africa. Its presence among a Yorkshire family dating back about 300 years was therefore quite unexpected.

    Since nothing more definitive can be inferred on the basis of the present data, exactly how and when this very rare African Y-chromosome was introduced into the otherwise perfectly indigenous English family will most likely remain unknown. On the basis of Y-STR analysis a Western African origin of this Y-chromosome is likely, despite its rarity. A more detailed surname analysis and a coalescence analysis based on Y-STR differences failed to yield a more exact coalescence date between the two families, although it is probably within a few generations (ie 100–150 years) before 1788. Based on this, it cannot be decided whether the introduction is due to a direct or indirect route. The former could relate to reports of Nubians in the Roman army defending the North territories; the latter could be associated with the later slave trade, which brought the first West Africans to England in 1555.6

    The study of King et al demonstrates that a Y-chromosome-only reconstruction of geographic origins can be seriously misleading. It also illustrates how a hitherto unknown secret pops up during a rather innocent pedigree reconstruction by means of Y-chromosome testing. As such it once again shows the importance of a general concept often ignored by participants of pedigree-based Y-testing: if you do not want to know, do not have yourself tested.

    Leave a comment:


  • GregKiroKH2
    replied
    I thought the article was interesting, Catherine. I thought your post was interesting too because I did not read the paper when I read the Scientific American article. I was pointing out "how people quote one another" is a little confusing. The Scientific American article is not as confusing as some students' papers I read. The original article by Bert Ely, Jamie Lee Wilson, Fatimah Jackson, and Bruce A Jackson was titled African-American mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups. I noticed in 2005 that I had mixed motifs of L1c and K in my HVR-I region. People said that it was impossible. I could only be one motif. I did not know about that. I just noticed that I could take the mutations from both groups. And I would almost get my mutations for my HVR-I region if I added two more mutations. Some of the earlier papers have recognized that American DNA did not always match African DNA. And idea of multiple African ethnic groups was interesting to me.

    Originally posted by Francois
    Greg,

    I am sory but I don't know what you mean. I found that article and posted it not realising that it had already been mentioned.

    Catherine

    Researchers report that mitochondrial DNA isolated from African-Americans matched up to distinct African ethnic groups in fewer than 10 percent of cases, based on a partial database of African DNA samples. October 13, 2006

    http://www.sciam.com/article.cfm?cha...B083414B7F00A7
    Consequently, common mtDNA haplotypes are shared among multiple ethnic groups. . . .

    When two independent African-American samples were analyzed, more than half of the sampled HVS-I mtDNA haplotypes exactly matched common haplotypes that were shared among multiple African ethnic groups. Another 40% did not match any sequence in the database, and fewer than 10% were an exact match to a sequence from a single African ethnic group.

    Received 31 May 2006

    http://www.biomedcentral.com/1741-7007/4/34

    Leave a comment:


  • Francois
    replied
    Greg,

    I am sory but I don't know what you mean. I found that article and posted it not realising that it had already been mentioned.

    Catherine


    Originally posted by GregKiroKH2
    Did he quote the abstract? I am reading more essays like this. When does a paraphrase really becomes better than a quote. Now, people are wonder why peacocks have tails, and men do not.

    Leave a comment:


  • GregKiroKH2
    replied
    Did he quote the abstract? I am reading more essays like this. When does a paraphrase really becomes better than a quote. Now, people are wonder why peacocks have tails, and men do not.

    Originally posted by casadecoqui
    Hello, Catherine:

    This article was mentioned in this POST

    when it first came out. I happen to know Dr. Jackson and Dr. Ely has visited my brother in Puerto Rico.

    Leave a comment:


  • casadecoqui
    replied
    Hello, Catherine:

    This article was mentioned in this POST

    when it first came out. I happen to know Dr. Jackson and Dr. Ely has visited my brother in Puerto Rico.

    Originally posted by Francois
    I thought this article might interest some of you:
    http://www.biomedcentral.com/1741-7007/4/34

    Catherine

    Leave a comment:


  • Francois
    replied
    African American mitochondrial DNAs often match mtDNAs found in multiple African ethn

    I thought this article might interest some of you:
    http://www.biomedcentral.com/1741-7007/4/34

    Catherine

    Leave a comment:

Working...
X