DNA, Ethnicity, Genetics and Genealogy: Mapping History and Culture with Haplogroup Studies and Surname Research

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DNA, Ethnicity, Genetics and Genealogy Mapping
History and Culture with Haplogroup Studies and
Surname Research

• Workshop at Fourth International Conference on
  Diversity, Los Angeles, Tuesday, July 6, 5-6
  p.m., Rm. 9, Conference Center, UCLA Sunset
  Village

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Researching Your Anthropogenealogy and Family
Ethnicity with DNA

• Presentation by
• Donald Panther-Yates
• DNA Consulting for History Genealogy

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Introduction

• Walk through steps in researching
• Direct male line (surname)
• Matrilineal deep history (mtDNA)
• Explain usefulness of gene banks
• Y-STR Haplotype Reference Db
• Cambridge Reference Sequence
• Not to define ethnicity, not technical
• About dnaconsulting.ws

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Topics of Discussion

• Definitions
• History of
• genealogy by genetics
• DNA-based anthropogenealogy
• Y-chromosomal route
• mtDNA route
• DNA Prints and other methods
• Examples

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Y Chromosome

• One of the two sex chromosomes, X and Y. The Y
  chromosome passes down from father to son.
  Females don't receive it. The fact that the Y
  chromosome goes down the paternal line is what
  makes it valuable for genealogy studies, since in
  general it follows a surname line.

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X Chromosome

• X is the sex chromosome that is present in both
  sexes singly in males and doubly in females.

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Inheritance Chart
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Branches and Twigs

• Haplogroups are the descents or mega-families
  that characterized early human migrations. They
  are normally associated with geographical
  regions. Examples R1b (Western Atlantic
  European), I (northern Europe), J (Jewish, Middle
  Eastern).
• Haplotype One person's set of values for the
  markers that have been tested. Two individuals
  that match on all markers but one, have two
  distinct haplotypes. (One-step mutation)

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Markers

• Markers are the site that is tested on the
  chromosome. Also known as sites, or loci. Names
  like DYS 390, DYS 285a.
• Scores or values on each marker are determined by
  how many STRs the double helix amino acids form
  Short Tandem Repeats. Also called alleles.
• STR - Short Tandem RepeatsKnown also as
  microsatellite, an STR is a short DNA motif
  (pattern) repeated in tandem. ATGC repeated
  eleven times would give the marker a value of 11.
  

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What is a gene?

• Allele Alternative form of a gene. One of the
  different forms of a gene that can exist at a
  single locus .
• Bases
• Adenine is the "A" of the four bases in DNA that
  make up the letters ATGC. The other bases are
  thiamine (T), guanine (G) and cytosine (C).
  Adenine always pairs with thiamine, guanine with
  cytosine.

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Mutation

• Mutation A heritable change that may occur in a
  gene in the form of a chemical rearrangement, or
  a partial loss or gain of genetic material,
  leading to a different number of repeats of a
  certain sequence (male) or change of one of the
  bases in a sequence (female). Mutation rate
  The rate at which a mutation can happen.

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Brief History of DNA Testing

• Gregor Mendel (19th cent.)
• Charles Darwin fils and cousin marriage
• Watson Crick (double helix, 1953)
• Biotechnology (1970s-80s)
• Cavalli-Sforza
• Human Genome Project
• Cohen gene (1997)

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Skorecki et al. 1997

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• Skorecki K, Selig S, Blazer S, Bradman R, Bradman
  N, Waburton PJ, Ismajlowicz M, Hammer MF (Jan.
  1997).Y chromosomes of Jewish priests. Nature
  2385(6611)32. 611)32.

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Recent Developments

• Brian Sykes
• Family Tree DNA
• Hammer Nomenclature
• Y-STR Haplotype Ref. Database
• Cambridge Reference Sequence
• Mitomap at Emory
• Melungeon DNA Project by Elizabeth Hirschman
• DNA Consulting for History Genealogy
• Prominent Researchers

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1. Verify the raw data for 12 target alleles from
the original lab report source.2. Control for
laboratory-specific testing parameters, known
validity and reliability issues, and
nomenclature.3. Perform a global search in the
Y-STR Database for the haplotype. a. Search for
truncated or mutational matches if
unsatisfactory yield. b. Compute descriptive
statistics for relevant countries. c. Establish
bivariate research theses. d. Determine
patterns, models, correlations, and other
inferential statistics. e. Control for
fast-moving markers and different mutation rates
and estimate most recent common ancestor. f.
Estimate risk factor of non-paternity events in
line.

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4. Compare search results with the other
available sequence databases (Ybase, Sorenson,
Family Tree DNA) a. Repeat steps 3a.-3f, if
necessary. 5. Search DNA Surname Projects. a.
Correlate branches or allonymic (other surname)
genealogies. b. Repeat steps 3a.-3f., if
necessary. 6. Conduct chronological interactive
search in relevant genealogy forums and e-mail
discussion list threads at Rootsweb and other
sites.

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7. Search WorldCat for archival papers, special
collection materials, and unique titles.8. Check
unpublished or password-protected databases,
including a. Subscriber-based information at
Ancestry.com b. Melungeon DNA Surname Project
(unpublished) c. JewishGen (need research
code) d. Scottish Clans (partially private) e.
Rabbinical genealogies (largely private) f.
Native American genealogies (usually requires
e-mail correspondence with owners) g. Human
Genome Project (requires inputting correct gene
sequence and glossary term) h. PubMed at the
National Library of Medicine (may require
publisher's password) i. Linkage literature and
deep history of genotype (highly specialized).

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9. Read any library articles or order any
required extra materials such as interlibrary
loan books. 10. Adjust inferences and retest
research thesis. 11. Conduct general Internet
keyword and natural phrase searches. 12.
Assemble data, design report, identify relevant
standard definitions, maps, scientific
boilerplate, disclaimers and notes, write thesis
and customized highlights. 13. Compose in HTML,
with correct links, illustrations, charts and
references. 14. Save file in sendable format
(usually zipped), back up, and store.

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Atlantic Modal Haplotype

• DYS388 12DYS390 24DYS391 11DYS392 13DYS393
  13DYS394 14 (also known as DYS19)
• If you have one mutation in either direction,
  then you are AMH 1.15. The AMH 1.15 haplotype is
  also referred to as the Atlantic Modal Cluster or
  AMC. Generally 1.15 puts you in haplogroup 1
  (H1), but not always.

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Y-STR Haplogroups
C
I
R1a1
R1b
E3b
J
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C
I
R1a1
E3b
J
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MtDNA Haplogroups
J
I
N
H
A, B, C, D, X
K
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Single Nucleotide Polymorphisms

• SNPs are used to
• Determine/confirm haplogroup affiliation
• Find Cohanim pattern (in J2)
• Subdivide haplogroups into sub-haplogroups,
  subclades (I1b2, I1b, K1, K2)
• Drug research, protein coding, disease
  linkage/screening, and gene therapy

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Other Methods

• Genetic profile (DNA Print)
• Human Lymphocyte Antigens
• Polymorphic Alu insertions
• No practical way to test cross-over lines of
  descent
• Ancient DNA (problematical)

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Cooper Haplotype in Y-STR Reference Database

• SNP test by FTDNA indicates R1b
• Hundreds of surname matches
• England modal country match
• Matched
• Elizabeth Hirschman (Caldwell)
• My wifes Ramey cousin
• Much of Clan Stewart

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Cooper Haplotype Distribution
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Nina Jo Newberry with son Ken
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Newberry Distribution in Y-STR Db
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Frequencies of Haplogroup I and Sub-haplogroup
I1a in Select European Populations

• French (Low Normandy) 24/12
• South Sweden 41/36
• Germany 38/25
• Saami (Finland) 31/29
• Portuguese 5/1.3
• English 18/NA
• Jewish 1/1
• Source Rootsi et al (2004)

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Research Hypothesis Tested by Inferential
Statistics from Forensic DNA Data

• Traced backward from
• N.C.
• New England
• Warwickshire, England
• Normandy
• Saxony
• Denmark

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Thorny Issues

• Non-paternity Events
• Mutation rates and MRCA
• Convergence and ancient DNA
• Surname homology (isonymy)
• Millions of lineages in one person
• Non-random mating, cousin marriage
• Importance of patrilinear inheritance