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Racial-variety Links Reference Shelf

  1. Aug 28, 2004 #1

    marcus

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    This thread is to collect links providing possibly useful information about human (respectively dog) racial (respectively breed) variety.
    other domesticated animals such as horses may sometimes appear.

    it is not intended to focus on issues and problems related to any one particular genetic group of people such as Finns, Maori, Han Chinese, or African-Americans (assuming these are indeed meaningful categories), or on any one particular breed of dog.

    An effort will be made to have the viewpoint international rather than being enmired in some limited US perspective or some other country's point of view.

    General links will be provided pointing out the dangers of having any races at all----genocide links---but the focus is not intended to be on dangers.

    IMO we have been getting a remarkable bunch of information lately at PF and I dont want to lose track of it and forget where the links are.

    TAXONOMY (courtesy ian)
    https://www.physicsforums.com/showthread.php?p=290880#post290880

    I understand that, in the traditional scheme of taxonomy, race is equated with sub-species (the two terms are synonymous). Divisions within a single race or subspecies are called varieties. Modern Human is a subspecies (race) of Homo Sapiens. Therefore technically one must go down one rank step in the classfication scheme when cataloging sub-populations within Modern Human. According to traditional taxonomy such a sub-population should be called a variety.

    Taxonomy is just one traditional discipline and we do not have to adhere strictly to its terminology. But there it is: to a conventional taxonomist accustomed to classifying other animals and plants, what might in some other context have been called a race is more apt to be called a variety.

    If the domestic dog is a subspecies (rather than a true species), then taxonomically-speaking breeds would also be called varieties.

    I must also acknowledge the possibility that the centuries-old classification system of Taxonomy may be destined to fail and that modern tools for analysing human DNA variety and organizing the information may necessarily involve innovative data structures. I got some hints of this in the papers people gave me to read.

    SAMPLE PAPERS in no particular order

    Heidi G. Parker, Lisa V. Kim, Nathan B. Sutter, Scott Carlson, Travis D. Lorentzen, Tiffany B. Malek, Gary S. Johnson, Hawkins B. DeFrance, Elaine A. Ostrander, Leonid Kruglyak
    Genetic Structure of the Purebred Domestic Dog
    Science (21 May 2004, vol 304 page 1160)
    http://www.akcchf.org/news/press/releases/2004/dogbreeds.pdf


    "From many recent article by Cavalli-Sforza, it seems that gene flow can be perceived and assessed but distinct groups can be distinguished."

    Mansoor A, Mazhar K, Khaliq S, Hameed A, Rehman S, Siddiqi S, Papaioannou M, Cavalli-Sforza LL, Mehdi SQ, Ayub Q.
    Investigation of the Greek ancestry of populations from northern Pakistan.
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=14986106

    Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA.
    A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes.
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=11910562

    Ayub Q, Mansoor A, Ismail M, Khaliq S, Mohyuddin A, Hameed A, Mazhar K, Rehman S, Siddiqi S, Papaioannou M, Piazza A, Cavalli-Sforza LL, Mehdi SQ.
    Reconstruction of human evolutionary tree using polymorphic autosomal microsatellites.
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=14533184

    Jin L, Baskett ML, Cavalli-Sforza LL, Zhivotovsky LA, Feldman MW, Rosenberg NA.
    Microsatellite evolution in modern humans: a comparison of two data sets from the same populations.
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=11246466

    "In both studies, Cavalli-Sforza team show a clear and significant clustering (6) of geographically related population. Cavalli-Sforza et al. also talk about the admixing of some geographically closed groups in African and Pakistani,.."

    I suspect that races are for most of us still somewhat vague and "sociological" classifications. the necessary DNA cataloging to reveal the human family tree in some objective reliable way seems to be in its early stages. So this is a border area between sociology and biology, where the older subjective and socially established terms may be replaced by more objective ones. there may also be many people whom no DNA algorithm can classify and who are therefore objectively raceless, while there may be others whose genes can be recognized and identified within a tree or web of categories.

    Someone recently supplied a link about Tiger Woods. for the time being he can serve to symbolize for us a person who might eventually prove to be genetically unclassifiable.
    [put Tiger Woods link here]

    so we have a mix of biology and sociology here and I chose to locate this link-basket thread in sociology forum.

    Here's something about lactase I couldnt make anything out of
    Mulcare et al---Re:Lactose tolerance Masai vs western Europe
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=15106124
     
    Last edited: Aug 29, 2004
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  3. Aug 29, 2004 #2

    marcus

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  4. Aug 29, 2004 #3

    marcus

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    definitions

    definitions came up in another thread courtesy ian
    the source given for the definitions is the European Union
    reference links are provided

    one sees that the "specialty" meaning, or technical meaning in a scientific taxonomomy context, is the same for the two words.
    Race = Sub-species
    and the next lower rank classification term is variety.
     
  5. Aug 29, 2004 #4

    marcus

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    When I first listed these sample articles one of the points I wanted to make was that the research was recent, often this year, and to give some suggestion as to who was doing it---the names of the researchers. But I neglected to put years by most of the articles. You can see several 2003 or 2004 here.

    Heidi G. Parker, Lisa V. Kim, Nathan B. Sutter, Scott Carlson, Travis D. Lorentzen, Tiffany B. Malek, Gary S. Johnson, Hawkins B. DeFrance, Elaine A. Ostrander, Leonid Kruglyak
    Genetic Structure of the Purebred Domestic Dog
    (2004, Science (21 May, vol 304 page 1160)
    http://www.akcchf.org/news/press/releases/2004/dogbreeds.pdf

    Mansoor A, Mazhar K, Khaliq S, Hameed A, Rehman S, Siddiqi S, Papaioannou M, Cavalli-Sforza LL, Mehdi SQ, Ayub Q.
    Investigation of the Greek ancestry of populations from northern Pakistan.(2004, Human Genetics)
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=14986106

    Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA.
    A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. (2002, American Journal of Human Genetics)
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=11910562

    Ayub Q, Mansoor A, Ismail M, Khaliq S, Mohyuddin A, Hameed A, Mazhar K, Rehman S, Siddiqi S, Papaioannou M, Piazza A, Cavalli-Sforza LL, Mehdi SQ.
    Reconstruction of human evolutionary tree using polymorphic autosomal microsatellites.(2003, American Journal of Physical Anthropology)
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=14533184

    Jin L, Baskett ML, Cavalli-Sforza LL, Zhivotovsky LA, Feldman MW, Rosenberg NA.
    Microsatellite evolution in modern humans: a comparison of two data sets from the same populations.(2000, Annals of Human Genetics)
    http://www.ncbi.nlm.nih.gov/entrez/...ve&db=pubmed&dopt=Abstract&list_uids=11246466
     
    Last edited: Aug 29, 2004
  6. Sep 2, 2004 #5

    marcus

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    plodding on with it
    anybody have more links?
    this has a couple of tables from the LLCavalli-S article in a 1991 Scientific American "Genes, Peoples, and Languages"
    http://www.friesian.com/trees.htm

    this one is about the likely separateness of Neanderthal. (still not a settlled question)
    http://www.ou.edu/cas/zoology/Courses/3333/sci-neanderthal-dna.html

    this is a cute website by a mathematician who just likes algorithms which construct phylogenetic trees. he is Dave Joyce and is at a place called Clarke U. in Massachusets. he has put in some Java applets that you can get to produce trees.
    http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html

    at stanford there is an anthropological geneticist named
    Joanna L. Mountain, and she has the "Mountain Laboratory of Anthropological Genetics"
    http://www.stanford.edu/group/mountainlab/
    (note that LLCavalli-S is also at Stanford, Joanna might be a protege
    or someone he brought there)
     
    Last edited: Sep 2, 2004
  7. Sep 2, 2004 #6

    marcus

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    a fascinating-looking list of publications (some text on line)
    http://www.stanford.edu/group/mountainlab/research/publications.html
    much coauthored by LLCS and JMountain.

    a recent (2003) statement of research purpose, by Joanna Mountain:

    "The current focus of the Mountain Lab is upon the highly informative but difficult to detect human variation found at the level of DNA. While not easily observed, DNA variation stores a great deal of information regarding the population processes of human history, as well as the evolution of our morphology, physiology, and behavior. We are currently surveying the maternally and paternally inherited genetic variation of a set of linguistically diverse peoples of Tanzania, addressing questions regarding the origins of our species, linguistic evolution, and the population history of East Africa. We are also developing a new set of genetic systems. These systems have already proven to be informative regarding major human migrations and population bottlenecks throughout the last 100,000 years of human history; we believe they will also be valuable within medical genetics research.


    More broadly speaking, our areas of research interest include: the origins of modern humans; comparisons of genetic and linguistic variation among human populations; ethical issues regarding human genetics; phenotype and the interactions among genotype, environment, and culture; biology and concepts of race; the extent to which genetic data can reveal details of human history; the origins of and relationships among the peoples of Africa, particularly East Africa; the development of statistical tools for analyzing a variety of human population genetic data; and, comparisons of the genetic variation of ancient and living peoples.


    For more information about specific Mountain Laboratory research projects, please select from the list on the left"
    http://www.stanford.edu/group/mountainlab/research/index.html

    at this index, clicking on "Race, Ethnicity, Genetic Variations" gets you to
    *

    "Race, Ethnicity, and Genetic Variation
    *
    Geneticists have understood for thirty years or more that the greatest proportion of genetic variation lies within human populations, however those populations are defined. Recently, however, the question of the extent of the correspondence between genetic variation and ethnic ancestry has arisen in a number of contexts (e.g. medicine, forensics, public policy, the search by individuals for information regarding their ancestry). Members of the Mountain lab are interested in exploring the correspondence between patterns of human population genetic structure and patterns of cultural diversity, and the social implications of relating genetic variation and ethnicity. In medical genetics research, for instance, the search for a genetic basis for disease often begins with a focus upon an ethnically defined group with a particularly high frequency of that disease. The efficiency and social impact of this approach has yet to be explored fully."
    *
    http://www.stanford.edu/group/mountainlab/research/regv.html
    *
     
  8. Sep 2, 2004 #7

    marcus

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    a complete Joanna article (2002) on line

    Joanna seems very interested in methodology, that is, in developing powerful systems of genetic markers. At her lab's site she headlines this recent (2002) article which is fortunately available online in toto.

    SNPSTRs: Empirically Derived, Rapidly Typed, Autosomal Haplotypes for Inference of Population History and Mutational Processes
    Joanna L. Mountain, Alec Knight, Matthew Jobin, Christopher Gignoux, Adam Miller, Alice A. Lin, and Peter A. Underhill

    STR means the same as "microsatellite" ---same type thing the Dog Team used.
    STR means "short tandem repeat"
    SNP means "single nucleotide polymorphism"

    a good indicator of where this field is now and where it is going would be to scan the whole article. basically it looks like they are developing fast tools, and testing them

    a single SNPSTR consists of one segment containing one STR and at least one SNP. the authors say that you can find out quite a lot with just one SNPSTR but that the main idea is to use a bunch of SNPSTRs all at once.
    they say it's good for determining phylogenetic trees and learning history and typing people for improved medical treatment and all the usual stuff like that.

    the way to get the complete article is to go to
    http://www.stanford.edu/group/mountainlab/research/publications.html
    and find it on the menu, and click where it says "PDF"
    otherwise all you get is the abstract, or short summary.
     
    Last edited: Sep 2, 2004
  9. Sep 2, 2004 #8

    marcus

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    another Joanna article online

    this was published in Proc. National Academy of Sciences (1997)
    NAS is bigtime science, the title is somewhat Big Brother:

    Detecting immigration by using multilocus genotypes
    Bruce Rannala and Joanna L. Mountain

    "Abstract.-- Immigration is an important force shaping the social structure, evolution, and genetics of populations. A statistical method is presented that uses multilocus genotypes to identify individuals who are immigrants, or have recent immigrant ancestry. The method is appropriate for use with alloenzymes, micorsatellites, or restriction fragment length polymorphisms (RFLPs) and assumes linkage equilibrium among loci. Potential applications include studies of dispersal among natural populations of animals and plants, human evolutionary studies, and typing zoo animals of unknown origin (for use in captive breeding programs). The method is illustrated by analyzing RFLP genotypes in samples of humans from Australian, Japanese, New Guinean, and Senegalese populations. The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low."

    To get the PDF for the complete article you have to go to Joanna's "publications" page and look down the menu of her many articles and find
    one that says "PDF" and click there
    http://www.stanford.edu/group/mountainlab/research/publications.html
     
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