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Thread: Genetics 101: The Basics

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    Genetics 101: The Basics

    A fairly comprehensive guide I wrote for another website several months ago. Will be sporadically updated in keeping with the times (and user interest). Enjoy!




    What is genetic genealogy?

    Genetic genealogy is the implementation of DNA testing into the study of one's recent family history (genealogy). However, the tests employed in genetic genealogy are based on the same principles as the form of DNA testing utilised by scientists researching human migration patterns. Thus, wider inferences can be made through such data, including the origins of a particular population or group bound by a common factor.


    What DNA is analysed in genetic genealogy?

    The human genome is composed of 46 chromosomes; 44 of which are in pairs of 22 (non-sex chromosomes) with the last two, X and Y (sex chromosomes) completing the figure. Genetic genealogists usually have the following bits of genetic information tested;
    Y-Chromosome (Y-DNA) - A sex chromosome, of which one is typically carried by a man (XY). Inherited directly from the father, who in turn inherits it from theirs, and so forth. The Y-Chromosome mutates at a fairly regular rate at different sites, allowing fine-scale tracking lines of descent to be deduced.
    mitochondrial DNA (mtDNA) - Genetic information found in the mitochondria, the "energy source" of most plant and animal species (eukaryotes). mtDNA is not considered a part of the human genome. Carried by both men and women, although inherited directly from the maternal side in both cases. This is because paternal mitochondrion, which is fuels the male sperm at the stage of human conception, is attached to the tail and is "dropped" prior to the sperm's fertilisation of the female ovum. Therefore, female mitochondrial material is the only form found in the just-fertilised egg (zygote). Mutates at a slower rate than Y-DNA.

    Y-DNA and mtDNA therefore form the basis of determining paternal and maternal lines of descent respectively, as both are inherited in almost-identical forms from each parent.

    Other portions of the human genome that may serve the purposes of genetic genealogy;
    X-Chromosome (X-DNA) - A sex chromosome, carried by both men (XY) and women (XX). Much like mtDNA and Y-DNA, X-DNA is also inherited directly from the parents. Unlike both, however, X-DNA is liable to recombination, a process where two similar chromosomes cross over at certain points. As men inherit their mother's X-DNA, testing of this would reveal the general ancestry of the mother's parents. Females, on the other hand, inherit one X-Chromosome each from their parents.
    Autosomal DNA - The name given to the non-sex chromosomes (1-22). Autosomal DNA is inherited roughly equally from both parents in summation, although certain portions may be completely or mostly derived from one.


    What is a Haplogroup (and other jargon)?

    • Nucleotide; the structural units of DNA (as well as RNA). Four building blocks exist in the human genome, which is built entirely from the following; Adenine (A), Cytosine (C), Guanine (G) and Thymine (T).
    • Gene; a stretch of DNA that is inherited in an organism.
    • Allele; one or more forms of a gene through the presence of different nucleotides.
    • Chromosome; a complex structure of genes bound by several protein and enzymes.
    • SNP (Single-nucleotide polymorphism); site on a gene where a different allele may be found in the same species (i.e. T in a certain mouse gene location where others have an A). Has a basis in the analysis of all DNA forms. In Y-DNA analysis, SNP's are either positive (+) or negative (-) for a particular result.
    • STR (Short tandem repeat); positions on a stretch of genome that produce "spikes" of genetic repetition. In genetic genealogy, this is commonly associated with Y-DNA testing.
    • DYS; Former, outdated term for STR.
    • Haplotype; a string of common STR values on the same points between individuals.
    • Haplogroup; a genetic group that is defined by a haplotype and the same alleles at key SNP's. These are defined by a letter-number-letter-number etc. combination that gives information on the relative depth of a lineage (e.g. J > J2 > J2a > J2a4 > J2a4h). Used in both Y-DNA and mtDNA.
    • Clade - A single division in a haplogroup; nomenclature (naming order) is a single letter followed by a single number. For example, Y-DNA haplogroups R1 and R2 are both clades of R.
    • Subclade - Further divisions in a clade; nomenclature again follows a single letter-single number order, but the increasing length denotes the "depth" of the divisions. For instance, mtDNA haplogroup C4a1 is a subclade of C4, much the same way Y-DNA haplogroup Q1a3a is a subclade of Q1.
    • Backbone SNP test - An SNP test on a certain form of DNA (i.e. Y-DNA) that assures membership to a particular haplogroup.
    • CRS (Cambridge Reference Sequence); the complete sequencing of a European's mtDNA from the 70's that serves as the benchmark for all subsequent comparisons. The CRS sample belongs to mtDNA haplogroup H2a2a.
    • HVR (Hypervariable region); regions on mtDNA that are prone to mutations. Two panels are usually tested; HVR1 and 2.


    Further terms can be looked up on FTDNA's Glossary (https://www.familytreedna.com/learn/glossary/).


    How are the haplogroups arranged?

    Both Y-DNA and mtDNA haplogroups are arranged in an evolutionary tree with younger branches toward the bottom. Population geneticists used this information to confirm the Out of Africa theory has a genetic basis, as all modern human Y-DNA and mtDNA can be ultimately traced to a common ancestor in Africa. The common Y-DNA founder of all humans is dubbed "Y-Chromosomal Adam" whilst the common mtDNA founder is "mitochondrial Eve". Please note the names are of symbolic value and do not represent or support any religious belief, as both progenitors lived tens of thousands of years before the present day. For more information on each tree branch and the associated markers, please refer to the Wikipedia entries for both;
    Y-DNA (http://en.wikipedia.org/wiki/Human_Y...NA_haplogroups)
    mtDNA (http://en.wikipedia.org/wiki/Human_m...NA_haplogroups)


    Can you provide us with real-life examples of Y-DNA or mtDNA in complete nomenclature?

    Take for instance a sample that belongs to Y-DNA haplogroup G. As haplogroup G is defined by the SNP marker M201, this sample has to be positive (+) for it. Further testing of this sample shows they belong to the clade G1 as well, as they test +ve for the marker which defines G1, M342. Eager to tell if their sample belongs to any G1 subclade, the contributor tests for G1a (P20) and G1b (P76). Testing reveals their sample is -ve for P20 and +ve for P76, implying they belong to G1b. Shown in genealogist shorthand as the following;

    G1b (M201+ M342+ P76+)

    Mitochondrial data is also determined in a similar way, with certain mutations defining a certain haplogroup lineage. However, some of the mutations found on HVR1 or HVR2 panels do not help define a person's haplogroup. Instead, a fixed list of mutations associated with each haplogroup are cited with raw results. Please refer to the mtDNA Haplogroup Mutations page on FTDNA (http://www.familytreedna.com/mtDNA-H...Mutations.aspx). Detailed information on determining mtDNA haplogroups can also be found here (https://www.familytreedna.com/tr_mtDNAPlus.pdf).


    Does my DNA change per generation?

    As discussed previously, certain DNA change whereas others only mutate at a slow enough rate to track inheritance patterns. Y-DNA, mtDNA and X-DNA (in men) are inherited mostly intact from an individual's parents. Y-DNA mutates at a faster rate than mtDNA and is more useful in ascertaining genealogical relationships. Autosomal DNA is inherited roughly equally from both parents but sporadic mutation events are likely to happen in a very small scale, though nowhere near enough to dissolute any kinship based through genetic testing.

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    Great post! I would like to add some excellent videos. I found many people interested in genealogy who are frightened by the scientific details of DNA. The videos below are my first suggestions for those new to DNA:

    http://www.smgf.org/pages/animations.jspx

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  5. #3
    Thanks very useful. As a newbie mainly interested in British & European studies could anyone recommend a book on the history of the subject and enlarging on the basics above . I have read the basic stuff like Sykes , Oppenheimer, Cunliffe , Moffat & Wilson etc .
    I would also like to know the use of the letters M , S , P , etc and and if possible an explanation for what looks like unnecessary confusion in trees like M343 -P25-L23 ETC .
    Thanks in advance .

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    Quote Originally Posted by Colin View Post
    Thanks very useful. As a newbie mainly interested in British & European studies could anyone recommend a book on the history of the subject and enlarging on the basics above . I have read the basic stuff like Sykes , Oppenheimer, Cunliffe , Moffat & Wilson etc .
    I would also like to know the use of the letters M , S , P , etc and and if possible an explanation for what looks like unnecessary confusion in trees like M343 -P25-L23 ETC .
    Thanks in advance .
    The letter prefixes reflects which particular lab or research group has cataloged the SNP. As there is not (yet) a central curated repository for assigning SNP tags, some labs have assigned their own tags to the same SNP, i.e. L21 is exactly the same as M529, which is exactly the same as S145. Often and usually this superfluousness results from a pervasive academic policy of not releasing or communicating data to competing institutions or the public until a paper is published, in order to properly attribute credit to the researchers and their respective affiliated institutions.

    The list of each lab or research group's letter prefix is provided by http://www.isogg.org/tree/index.html

    DF = anonymous researcher using publicly available full-genome-sequence data, including 1000 Genomes Project data; named in honor of the DNA-Forums.org genetic genealogy community
    G = Verónica Gomes, IPATIMUP Instituto de Patologia e Imunologia Molecular da Universidade do Porto (Institute of Molecular Pathology and Immunology of the University of Porto)
    IMS-JST = Institute of Medical Science-Japan Science and Technology Agency
    KHS = Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology
    KL = Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    L = Thomas Krahn, MSc (Dipl.-Ing.) of Family Tree DNA's Genomics Research Center; snps named in honor of the late Leo Little
    M = Peter Underhill, Ph.D. of Stanford University
    N = The Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing
    P = Michael Hammer, Ph.D. of University of Arizona
    Page, PAGES or PS = David C. Page, Whitehead Institute for Biomedical Research
    PK = Biomedical and Genetic Engineering Laboratories, Islamabad, Pakistan
    S = James F. Wilson, D.Phil. at Edinburgh University
    TSC = Gudmundur A. Thorisson and Lincoln D. Stein, The SNP Consortium, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
    U = Lynn M. Sims, University of Central Florida; Dennis Garvey, Ph.D. Gonzaga University; and Jack Ballantyne, Ph.D., University of Central Florida
    V = Rosaria Scozzari and Fulvio Cruciani, Universitŕ "La Sapienza", Rome, Italy
    Z = G. Magoon, Richard Rocca, David F. Reynolds, Bonnie Schrack, Peter M. Op den Velde Boots, Ray H. Banks, and an anonymous individual, independent researchers of 1000 Genomes Project data and Thomas Krahn, MSc (Dipl.-Ing.) of Family Tree DNA's Genomics Research Center, with support from the DNA-Forums.org genetic genealogy community
    Each SNP catalog ID correlates to a ChrY locus coordinate and mutational state, listed at http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html. However, not all SNPs have been made public in this manner; many are still unpublished or are in an early research phase.
    Last edited by VinceT; 11-08-2012 at 08:06 AM.

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    Perfect , thanks Vincent .

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    For anyone interested in an expansion on the above I have created a free online Beginner's Guide to Genetic Genealogy
    http://tinyurl.com/geneticgenealogyguide
    Kelly Wheaton

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    good post ! really useful information... Thanks for sharing...

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    I have a question regarding how far back DNA relative finders like 23andme can go. What is the maximum age / number of generations a shared segment can stay intact?
    I've once read in the comments section of a 23andme article that it's about 300 years max. I mean from a mathematical view point shared segments can't go back very far into the past considering that the number of once ancestors (and the amount of recombination) increases exponentially with every generation one goes back.

    If we assume that a generation is about 20-25 years that would amount to 12-15 generations in 300 years.
    1 generation back: 2 parents
    2 generations back: 4 grandparents
    ....
    12 generations back: 4.096 ancestors
    ...
    15 generations back: 32.768 ancestors
    (of course there will be lots of interrelatedness and the number of nonrecurring ancestors will be much lower)

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    Quote Originally Posted by Sangarius View Post
    I have a question regarding how far back DNA relative finders like 23andme can go. What is the maximum age / number of generations a shared segment can stay intact?
    I've once read in the comments section of a 23andme article that it's about 300 years max. I mean from a mathematical view point shared segments can't go back very far into the past considering that the number of once ancestors (and the amount of recombination) increases exponentially with every generation one goes back.
    We can actually derive the answer from working backwards based on defining what the smallest shared segment is. I don't know what the bottom threshold is, but it's 0.08% on my RF.

    Working with that, RF can go back 10-11 generations in detecting a shared segment with a given individual. It's 10-11 because 0.08% falls in-between those two generations and I'm uncertain what the threshold actually is (probably isn't any lower than 0.05%, which is equivalent to 11 generations anyway).

    If we presume a generation is between 20-30 years, we'd be looking at an absolute lower bound of 200 years and an absolute upper bound of 330 years. Take the midway point of both and that's around 263 years. Which isn't far off the 300 year figure you read in the comments section.

    As the numbers coincide with another, RF probably picks up connections going as far back as the early 17th century. Hope you've found that useful (basically confirming what you read).

    Code:
    0	100% (you / monozygotic twin)
    1	50% (parent)
    2 	25% (grandparent)
    3	12.5%
    4	6.25%
    5	3.125%
    6	1.5625%
    7	0.78125%
    8	0.390625%
    9	0.1953125%
    10	0.09765625%
    11	0.048828125%

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    In this forum there is alot of vocabulary which hard to find a proper definition on making it hard for newbies to understand. So there should be a glossary for populations (eg ENF, EHG etc) and for slang used on forums such (eg Noise) or other words that might be confusing. Many of the terms are used throughout the forum so a glossary will make a good reference.

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