Announcement

Collapse
No announcement yet.

Articles and Interesting Links

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

  • #46
    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

    Comment


    • #47
      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: p.de_knijff@lumc.nl

      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.

      Comment


      • #48
        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

        Comment


        • #49
          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

          Comment


          • #50
            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?

            Comment


            • #51
              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

              Comment


              • #52
                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.

                Comment


                • #53
                  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.

                  Comment


                  • #54
                    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

                    Comment


                    • #55
                      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/

                      Comment


                      • #56
                        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 ]

                        Comment


                        • #57
                          EuroAfroAmericans and AfroAmericans and AsianAfroAmericans

                          Sex-biased gene flow in African Americans but not in American Caucasians

                          V.F. Gonçalves, F. Prosdocimi, L.S. Santos, J.M. Ortega and S.D.J. Pena
                          Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais,
                          Belo Horizonte, MG, Brasil
                          Corresponding author: S.D.J. Pena
                          E-mail: spena@dcc.ufmg.br

                          Genet. Mol. Res. 6 (2): 156-161 (2007)
                          Received March 14, 2007
                          Accepted March 14, 2007
                          Published May 9, 2007

                          ABSTRACT. We have previously shown evidence of strong sex-biased genetic blending in the founding and ongoing history of the Brazilian population, with the African and Amerindian contribution being highest from maternal lineages (as measured by mitochondrial DNA) and the European contribution foremost from paternal lineages (estimated from Y-chromosome haplogroups). The same phenomenon has been observed in several other Latin American countries, suggesting that it might constitute a universal characteristic of the Iberian colonization of the Americas. However, it has also recently been detected in the Black population of the United States. We thus wondered if the same could be observed in American Caucasians. To answer that question, we retrieved 1387 hypervariable I Caucasian mitochondrial DNA sequences from the FBI population database and established their haplogroups and continental geographical sources. In sharp contrast with the situation of the Caucasian population of Latin American countries, only 3.1% of the American Caucasian sequences had African and/or Amerindian origin. To explain this discrepancy we propose that the finding of elevated genomic contributions from European males and Amerindian or African females depends not only on the occurrence of directional mating, but also on the “racial” categorization of the children born from these relations. In this respect, social practices in Latin America and in the United States diverge considerably; in the former socially significant “races” are normally designated according to physical appearance, while in the latter descent appears to be the most important factor.

                          Key words: Mitochondrial DNA, Y-chromosome, African Americans, American Caucasians, Brazilians

                          Comment


                          • #58
                            Article on Y, X, autosomal and mtDNA in African Americans

                            Great Post Dra. Ana & Greg,
                            I'm not surprise with these findings. As more data is accumulated on those of us who do have these admixtures, I think the results will prove to be insightful. Thanks for the articles.
                            Denise

                            Comment


                            • #59
                              The Genographic Public Project mtDNA Database

                              Here a link to the article: https://www3.nationalgeographic.com/...PLOS_paper.pdf

                              I believe there a link to the database as well.

                              https://www3.nationalgeographic.com/...resources.html

                              Go to "the Get supplemental data" link, it is a xls (Microsoft Excel) format. I participated in the public database, I found my mtDNA markers and their final Haplogroup designation was L1c2 instead of L1*, however they when I go to my Genographic page they still have my haplogroup at L1*. Has anyone else read the paper and search the database?

                              Comment


                              • #60
                                The good thing about these sub-clades is that we can understand how our society became what it is today. Luckily for me, my R1b does not have many matches after 12 markers. Still, some of the older markers can tell us a unique story of history.

                                mutations tend to increase in value but not always

                                DYS 390 = 23, DYS 492 = 13
                                Northern Germany, Scandinavia, Frisian

                                S28+/492=14 seems to
                                represent deep ancestry among
                                the Celts of southern Germany and northern Italy

                                S28+/492=12 seems to
                                represent more northern Celt deep ancestry

                                R1b DYS 390, 391, 392 and 393
                                Atlantic Modal: 24, 11, 13, 13
                                NW Irish: 25, 11, 14, 13
                                Scottish: 24, 10 13, 13
                                Anglo-Saxon: 23, 11, 13, 13
                                N Italy 24, 10, 13, 14
                                L3 mtDNA Y-DNA related

                                M168 R1b separated from E3b
                                M89 R1b separated from G and I
                                M173 R1b separated from R1a

                                G2 al-Quraish 21, 10, 11, 15
                                E3b Levite 24, 10 (11), 11, 13
                                R1a 25, 10, 11, 13
                                DYS388 = 13
                                I1b2a 23, 10 (11), 11, 14 (15)
                                DYS388 =14, DYS19 = 14
                                I1a - Anglo-Saxon 22, 10, 11, 13
                                I1a-NORSE 23, 10, 11, 13


                                Originally posted by clarkedenise
                                Great Post Dra. Ana & Greg,
                                I'm not surprise with these findings. As more data is accumulated on those of us who do have these admixtures, I think the results will prove to be insightful. Thanks for the articles.
                                Denise

                                Comment

                                Working...
                                X