dna, ethnicity, genetics and genealogy: mapping history and culture with haplogroup studies and...

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

Researching Your Anthropogenealogy and Family Ethnicity with DNA

Presentation by

Donald Panther-Yates

DNA Consulting for History & Genealogy

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

Topics of Discussion Definitions History of

genealogy by genetics DNA-based

“anthropogenealogy” Y-chromosomal route mtDNA route DNA Prints and other methods Examples

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.

X ChromosomeX Chromosome

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

M8 + F8 M9 + F9 MA + FA MB + FB MC + FC MD + FD ME + FE MF + FF I I I I I I I I M4 …. + …. F4 M5 …. + …. F5 M6 …. + …. F6 M7 …. + …. F7 I I I I M2 …. …. …. + …. …. …. F2 M3 …. …. …. + …. …. …. F3 GrandFather I I GrandMother I I M1 …. …. …. …. …. …. …. + …. …. …. …. …. …. …. F1 Father I Mother I I I I Brother M0 F0 Sister

Inheritance ChartInheritance Chart

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)

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.

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.

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.

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)

Skorecki et al. 1997

Skorecki K, Selig S, Blazer S, Bradman R, Bradman N, Waburton PJ, Ismajlowicz M, Hammer MF (Jan. 1997).“Y chromosomes of Jewish priests.” Nature 2;385(6611):32. 611):32.

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

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.

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.

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).

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.

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.

Y-STR Haplogroups

CR1a1

R1b

I

E3b

J

CR1a1 I

E3b

J

MtDNA Haplogroups

J N

H

I

A, B, C, D, X

K

Single Nucleotide PolymorphismsSNPs 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

Other MethodsGenetic profile (DNA Print)Human Lymphocyte AntigensPolymorphic Alu insertionsNo practical way to test “cross-over” lines of descentAncient DNA (problematical)

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 wife’s Ramey cousin Much of Clan Stewart

Cooper Haplotype Distribution

Nina Jo Newberry with son Ken

“Newberry” Distribution in Y-STR Db

Frequencies of Haplogroup I and Sub-haplogroup I1a in Select European Populations

French (Low Normandy) 24/12South Sweden 41/36Germany 38/25Saami (Finland) 31/29Portuguese 5/1.3English 18/NAJewish 1/1

Source: Rootsi et al (2004)

Research Hypothesis Tested by Inferential Statistics from Forensic DNA Data

Traced backward fromN.C.New EnglandWarwickshire, EnglandNormandySaxonyDenmark

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