National Geographic Explorer: How to build an Ancient Man

CeCe Moore, at Your Genetic Genealogist, has a post on the recent National Geographic Explorer program on the reconstruction of the genetics of a Saqqaq male from Greenland, "How to Build an Ancient Man" This is a followup to the scientific article abstracted here: Gilbert et al., "Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland", Science 27 June 2008: 1787-1789. DOI:10.1126/science.1159750 . The article implies multiple entries into the Americas from Asia.

See the facial reconstruction of Inuq an ancient Saqqaq male from Greenland.

X Chromosome matches from 23andme

This chart is of my X Chromosome matches from Relative Finder and Ancestry Finder at 23andMe. The length of the line corresponds to the length of the match on the X chromosome. Because I am a male, I got one X chromosome from my mother.  She got an amalgam of the X chromosomes from her father and mother. I can only verify my relationship to three of the people on this chart.

SKD is my multiple 1st cousin and the relationship is through our mothers, who were sisters.  My 1st cousin and I share 6 of 8 great grandparents. We match at two locations on the X: 1-12, and 91-140.

LB and CF are 3rd cousins 1 remove and 2 removes, a mother and daughter. My 1st cousin and I share 4 of 16 GGreat grandparents with them, Swain, Ball, Kidd, and Stephens.  However, my 1st cousin does not match them or me at these locations on the X chromosome, but does match them on other chromosomes as I also do.

With HP, the link may be through the Hays/Hayes family of Overton and Fentress Co., Tennessee. HPs X line is from the same area. The mother of Maliza Stephens was Susan Hayes, and she and her husband, Zorababel Stephens, lived in Overton/Fentress Co., TN. This would subsume the links to LB and CF.

With three others, GA, JO, and CO, a mother and two of her sons, the relationship is unknown. My 1st cousin does share this match with them. We thought the relationship was on the Strunk/Strunck line, but that is not a direct line for them.

It is important to remember that a different cutoff is used for calling a match on the X chromosome between males, a male and a female, and between females:

Males: 200 SNPs, 1cM;
Male to Female: 600 SNPs, 6cM;
Female to Female: 1200 SNPs, 6cM.

This probably explains some match I have with females which do not show as a match for my female 1st cousin.

I am hoping to get some more 1st cousin matches to help to isolate matches to particular lines.

Here is a link to my pedigree charts:
Steven C Perkins 13 Generation Pedigree Charts 

FTDNA 7th Genetic Genealogy Conference

Family Tree DNA's 7th Genetic Genealogy Conference

The 7th Genetic Genealogy Conference for Family Tree DNA Group Administrators November 5-6, 2011
To be held at the Sheraton North Houston 15700 John F. Kennedy Boulevard Houston, TX 77032 (281) 442-5100
Book a Room at the Sheraton North Houston at a Discount
*The Sheraton website has a known issue with the Chrome browser. To visit their site please try another browser.

Featured Speakers

• Doron Behar, PhD
• Michael Hammer, PhD
• Steve Morse, author of the website "One Step Pages"
• Spencer Wells, PhD

X chromosome inheritance at 23andMe through Relative Finder and Ancestry Finder

The link above goes to a page that has charts for determining which ancestors contributed to your X chromosome. For a male, only his mother contributes an X chromosome. For a female both her mother and her father contribute X chromosomes. Parts of those chromosomes will be inactivated but the X can still be used for genealogical purposes.

I have 24 people who match me on the X chromosome at 23andMe through Relative Finder and Ancestry Finder. Neither FTDNA nor SMGF have published their X chromosome databases. GEDMATCH allows FTDNA customers to match their X chromosomes to other GEDMATCH participants. I haven't heard of anyone else having as many matches, but I am sure there must be someone who does. At this time I can only confirm three of the matches with one 1st cousin and with a 3rd cousin once removed and her daughter. I share a surname in the 1600s in Germany with a mother and her two sons. But since that surname is not contributing to the X chromosome before 1830, the assumption is that there is a closer link than that surname.

There are 5 and 6 generation charts for both males and females on the page. Below are the people, with their ancestor chart number, who would be on my 6 Generation Chart on the linked page with the percentage of X chromosome contribution expected from each.

1, myself
-------------
2 Denval Perkins 0%
3 Mary Ruth Ball 100%
------------
6 George Matt Ball 50%
7 Rosa Genetta Swain 50%
------------
12 Peter Coleman Ball 0%
13 Frances Strunk 50%
14 Thomas J Swain 25%
15 Elizabeth Kidd 25%
------------
26 Manoah Strunk 25%
27 Susana Cortina Davis 25%
28 Jesse D. Swain 0%
29 Elizabeth Ball 25%
30 John Kidd 12.5%
31 Maliza Stephens 12.5%
-------------
52 Abraham Strunk 0%
53 Abigail Pennington 25%
54 John Davis 12.5%
55 Frances Creekmore 12.5%
58 William Ball 12.5%
59 Charlotte May 12.5%
60 Elias Kidd 0%
61 Margaret Bagley 12.5%
62 Zorababel Stephens 6.25%
63 Susan Hayes 6.25%

Percentages are averages and usually can range from 0-100.

Having this chart filled out based on your sex can assist in identifying your X chromosome matches.

23andMe DNA test discount certificate: $50.00 off until 9 August 2011

To use this coupon, visit our online store and add an order to your cart. Click "I have a discount code" and enter the code below.
$50 Off

Coupon code: YG7XDH

Share with your friends!

(Valid for new customers only)

This works with either the $99 plus 12 months at $9 subscription, or with the $399 service without a subscription.

Comparison of 23andme Relative Finder, Ancestry Finder and FTDNA Family Finder results

I'll repeat a post I made at 23andme on comparing success rates at both:

======================================

Colonial American ancestry: Jamestown, Boston, Cambridge, Hartford, New Haven Colony, New Amsterdam, New Sweden, New Jersey, Pennsylvania. Then spread out to North Carolina, South Carolina, both pre-Rev War; then Tennessee and Kentucky, post-Rev War.

• at 23andme I have 1050 RF matches and have confirmed 7 of those.
• at FTDNA I have 175 FF matches and have confirmed 10 of those.
• Two of my confirmed matches have tested both 23andme RF and FTDNA FF.
• I have 20 separate X Chromosome matches in RF and AF. That counts repeated people only once.
• I have no immediate matches at FTDNA. I have 54 close matches and 121 speculative matches. My closest confirmed matches are two 4th cousins.
• I have two known 1st cousins at 23andme and two unresponsive 2nd cousins. My closest confirmed match at 23andme is with a 3rd cousin once removed and her daughter.

=======================

If you haven't done any tests I recommend starting at 23andme and then, when FTDNA opens the program, transferring your results to FTDNA. That way you get genealogical matches from both companies, you get mtDNA haplogroup and if a male, Y DNA haplogroup, and X chromosome matches at 23andme plus health info.

At FTDNA you get genealogy matches and when they get it ready, X chromosome matches. You have to pay separately for the Y DNA haplotype and haplogroup and the same for mtDNA. So from a cost perspective it is lower cost to start at 23andme and transfer to FTDNA UNLESS you also want detailed Y DNA /mtDNA readings.

Roots Into the Future: New Project at 23andMe for African American, Black, and African research

Roots Into the Future:

10,000 FREE DNA Test kits for persons of Sub-Saharan African Ancestry

A recent article in Wired Magazine highlighted how the genome revolution has been skipping most people in the world: 96% of participants in recent genomic studies trace most of their ancestry to Europe. Why? Statistical analysis is simpler in groups tracing ancestry to just one continental region so fewer individuals are needed to make discoveries. Although African Americans typically trace about 20% of their ancestry to Europe, studies to verify previous findings in this population have not been done for many diseases. Our understanding of how DNA influences disease risk in people with mostly non-European ancestry has a lot of catching up to do.
23andMe hopes to bridge this growing divide through Roots into the Future, a research initiative addressing the needs of the African American community. Our partners in the research initiative include Dr. Henry Louis Gates and the W.E.B. Du Bois Institute at Harvard, as well as advisors from academia, industry and the 23andMe community. Our goal is to enroll 10,000 participants who self-identify as African American, Black, or African in order to rapidly accelerate genetic research in the African American community.

Continues at http://spittoon.23andme.com/2011/07/26/roots-into-the-future/

See the Roots Into the Future website: https://www.23andme.com/roots/

23andColm: Some analysis you can do with your 23andMe result file

Colm O'Dushlaine, a genetics researcher, has been documenting his use of various tools to analyze his 23andme results. See this web site: https://sites.google.com/a/codushlaine.com/colm-o-dushlaine/23andcolm

The entry for Day 11 has a link to his EthnoAncestry Total Genomic Ancestry Classification report for those wondering what one looks like.

You can do the same analysis he is doing if you have access to UNIX/LINUX or can find a variant of the programs used for your operating system.

Update on 23andMe and FTDNA DNA matches

Today I have 160 matches at FTDNA in the Family Finder autosomal DNA database.

I have 998 matches in the 23andMe Relative Finder autosomal DNA database and around 700 unique matches in the Ancestry Finder database. 23andMe includes X chromosome matches which are not yet posted by FTDNA.

While I have more matches in the 23andme database, I have made more identifications of the ancestral couple in the FTDNA database. Testing with both companies remains the optimum strategy for finding genealogical connections.

Even though I have 10 surname projects at FTDNA, for autosomal and X chromosome DNA testing I recommend using 23andme first, and when they make it available, transferring your genome results to FTDNA to get matches against their database. This will cost the least for people in the USA.

The only other company I currently recommend is the Sorensen Molecular Genealogy Foundation, http://smgf.org/ They test Y DNA, mtDNA, autosomal DNA and X chromosome DNA. You can get tested for no cost if you meet their research requirements and submit a pedigree chart. However, there is no guarantee they will post your results on their system. They have made the Y DNA and mtDNA databases freely accessible on their website. It is anticipated they will do the same for autosomal and X chromosome DNA. They also sell access through GeneTree, http://www.genetree.com/ People who do not qualify for free DNA testing at SMGF, can pay for testing at GeneTree.

At this time, I am using DNA testing to verify my documented genealogy. I think it can be a very good check against one's paper genealogy.

FTDNA Summer DNA tests Sale

You must already be a customer of FTDNA to get these UPGRADE prices!

Family Tree DNA

Dear Project Administrator,

Since last summer's upgrade sale was such huge success, we thought we'd repeat history! Project Administrators like you played a very important role in last year's success by broadcasting the sale to project members. As your project members upgrade, the resolution of results and comparisons we provide greatly improves. So, please spread the word and we'll make this year's upgrade sale even bigger!

From June 15, 2011 through June 22, 2011, we will reduce the following prices.

         Summer Upgrade Sale
Family Finder  Was $289  Now $199
Y-DNA 12 to 25  Was $49  Now $35
Y-DNA 12 to 37  Was $99  Now $69
Y-DNA 12 to 67  Was $189  Now $148
Y-DNA 25 to 37  Was $49  Now $35
Y-DNA 25 to 67  Was $148  Now $114
Y-DNA 37 to 67  Was $99  Now $79
mt to FMS  Was $269  Now $229
mtPlus to FMS  Was $239  Now $199

To order an upgrade at these special prices your members can log into their personal pages with their kit number and password. Click on the "Special Offers" link found on the left-hand navigation bar. ALL ORDERS MUST BE PLACED AND PAID FOR BY MIDNIGHT, JUNE 22, 2011, TO RECEIVE THE SALE PRICE.

Family Tree DNA
© 2011 Genealogy by Genetics.

DNAGuide software demonstration

I have come across an interesting short slide set on DNAGuide software by Alice Rathjen.

A presentation she made at April 28th at World DNA Day and Genome Day in Dalian, China is available on her blog DNA Times.

Analysing 23andMe Relative Finder results: Always take a second look.

See corrected text below: NOT my Father's mtDNA haplotype.

Several months ago I got a a 22cM 23andMe Relative Finder match with A. Her surname was one in my paternal grandmother's ancestry. She was a predicted 4th cousin with a range of 3rd to 7th. We compared ancestry charts and determined we shared two lines on her Father's side. We were both half 5th cousins once removed and half 6th cousins on that surname. I was descended from a husband and one wife and she was descended from the other wife on two lines.

This week I noticed her father's results had arrived and I did not have a match with him. Since a 22cM match seemed too large to be Identical by State and/or fit into those situations where one has a match with a child but not a parent, I looked at the link to her updated Ancestry tree and found that she and I had a 5th cousin relationship on her Mother's side also through my paternal grandmother.

In this case she was a direct female line descendant of my Father's direct female line ancestor, so her mtDNA was the same as my paternal grandmother and my Father. This filled in one of my missing mtDNA haplogroups and indicated that the first relationships found probably were not the ones that passed on the genetic match.

We do share some other surnames but can't find a relationship yet on those other lines. Even if there are relationships on the other lines they would be further back than the closest one we now have.

Please let me know of any problems with my analysis.

DNA haplogroups of European Royalty

The following list of DNA haplogroups of European Royalty is found on the EUpedia site: http://www.eupedia.com/forum/showthread.php?25236-Haplogroups-of-European-kings-and-queens

I cannot vouch for the accuracy of the posting, but it may be of interest to genetic genealogists.

FTDNA 36 Hour Sale

If you have any problems contact FTDNA at info@ftdna.com or call the number on their web page linked above.

Family Tree DNA 36 hour sale on DNA tests

From the FTDNA Facebook Page:
Coupon Code: DNADAY2011
Share · Public Event
http://www.familytreedna.com
Created By Family Tree DNA

DNA Day is April 15th! Starting at 12:00 PM on April 14th, join the celebration!

New customers:
Y-DNA12……. $59
Y-DNA37……. $129
...mtDNA………. $59
Family Finder… $199
Family Finder + Y-DNA12….. $258
Family Finder + mtDNA…….. $258
Family Finder + mtFullSequence + Y-DNA67 …. $657

Upgrades:
Y-DNA12 add-on ….. $59
Y-DNA12 to 37…….. $69
Y-DNA37 to 67…….. $79
Y-DNA12 to 67…….. $148
mtDNA add-on …….. $59
mtFull Sequence upgrade ….. $199

To take advantage of these promotional prices use the coupon code: DNADAY2011

The coupon code will expire on Friday at midnight (CST).

Please note, the Y-DNA67 to 111 upgrade will remain at the introductory rate of $101 (no coupon necessary) until the end of this promotion. The price will be $129 going forward.

Payment must be received at the time of the order. Valid only on products listed. No substitutions. This promotion was announced in advance, therefore no adjustments will be made on previous purchases. Offer valid from 12:00 PM CST on Thursday, April 14, until 11:59 PM CST on April 15, 2011.

This promotion is not valid in combination with any other promotions. Family Tree DNA reserves the right to cancel any order due to unauthorized or ineligible use of discounts and to modify or cancel these promotional discounts due to system error or unforeseen problems. Subject to change without notice.

Family Tree DNA switches autosomal DNA tests to the Illumina chip

In February FTDNA announced that they were switching to the Illumina OMNI test chip for their Family Finder autosomal DNA test. Since then people have been gradually getting their test results from the new chip. At this time I have 122 matches from the old Affimatrix chip and 110 from the Illumina chip. They are not all the same and I will be comparing the results from each chip.

In the past I have advised people to do their first autosomal DNA test at 23andme.com since they had a lower cost and they compared the X chromosome, which FTDNA does not currently do. In addition, males got their Y DNA haplogroup and their mtDNA haplogroup. Females got the mtDNA haplogroup. Since FTDNA had announced that they would compare 23andme results to FTDNA Family Finder results, this seemed to be the most cost-effective testing protocol to follow. The switch by FTDNA should make the comparison of results much easier since 23andme also uses an Illumina test chip.

Early DNA Day Sale at 23andMe.com

23andMe will have a 1 day sale starting at 12:00 am P.S.T. on 11 April, 2011, ending that day at 11:59 pm PST. The sale price will be $108.00 for the test and one year of access to your test results. After one year, you will need to pay $9.00 per month to continue to have additional genealogical and health results added to your test results.

The current price is $199.00 for the test, plus $9.00 per month for at least 12 months to access to your results.

Matches at 23andMe.com and at FTDNA.com

My matches at 23andMe:
Relative Finder: 753
New in the last 7 days (19)
New in the last 30 days (78)
Sharing Genomes (198)
Public Matches (59)
Contact Sent (478)
Inbound Contact (0)
Contact Accepted (179)
Contact Declined (28)
Matches to Contact (25)
Introduction Canceled (0)

FTDNA:
Family Finder:
Affymetrix: 122
Illumina: 56

At 23andMe I have a known 1st cousin, a predicted 2nd cousin who has not responded to emails, and then several confirmed 3rd cousins, 6th cousins and 10th cousins.

At FTDNA I have no higher than predicted 3rd cousin matches and the highest confirmed match is with a 4th cousin.

Genetic Diversity among the Founders of Newfoundland

Mitogenomic and microsatellite variation in descendants of the founder population of Newfoundland: high genetic diversity in an historically isolated population.
Pope et al. (2011)

Abstract:
The island of Newfoundland, the first of England's overseas colonies, was settled from the 17th century onward by restricted numbers of English, Irish, and French immigrants, in small ``outport'' communities that have maintained geographic, religious, and linguistic isolation to the latest generations.
To measure the extent of modification and loss of genetic variation through founder effect, drift, and inbreeding in this historically isolated population, we analyzed the complete mitochondrial DNA (mtDNA) genomes and 14 microsatellite loci from each of 27 individuals with matrilineal ancestries extending to the colonial period. Every individual has a unique mtDNA genome sequence. All but one of these genomes are assignable to one of five major (H,J,K,T, and U) or minor (I) European haplogroups. The possibility of homoplasy at single nucleotide polymorphism (SNP) sites that define subtypes within the H haplogroup is discussed. Observed haplogroup proportions do not differ significantly from those of western Europeans or between English and Irish Newfoundlanders. The exceptional individual is a member of haplogroup A2, who appears to be the descendant of a Mi'kmaq First Nations mother and a French father, a common marriage pattern in the early settlement of Newfoundland.
Microsatellite diversity is high (HE = 0.763), unstructured with respect to mtDNA haplotype or ethnicity, and there is no evidence of linkage disequilibrium. There is a small but significant degree of inbreeding (FIS = 0.0174). Collection of whole mtDNA genome data was facilitated by the use of microarray sequencing, and we describe a simple algorithm that is 99.67% efficient for sequence recovery.

http://www.mun.ca/biology/scarr/Pope,_Carr,_Smith,_&_Marshall_2011_Genome_54,110.pdf

My new 23andMe matches since version 3 results have started coming in

Late Tuesday I had 594 matches in Relative Finder at 23andMe. On Wednesday I had 624, and on Thursday I had 655. Friday I added 2 more and 2 more again today, Saturday, 29 January, for a total of 659. Only one match has been at the 3rd cousin level. The rest have been in the 4th to 5th cousin range with a few "Distant Cousins" thrown in. One person had 5 links to me and one person had a single 50cm link. So far 3 people have accepted contact and shared genomes.

I'll post periodic updates as more matches come in.

Comparison of Verison 3 results to Version 2 at 23andme

CeCe Moore has reported on her quick comparison of her version 3 results to her version 2 results from 23andMe. According to an analysis by Jim McMillan there are approximately 30K SNPs that were in version 2 that are not in version 3.

Here is the link:Update on 23andMe's v3 results: Relative Finder comparison and ~30,000 v2 locations missing from v3

Combining document genealogy with genetic genealogy: "The man who wasn't John CharlesBrown "

One of the goals of this site is to show how to use genetic genealogy to assist with document genealogy. Randy Majors has a recent post that does just that. Read it on his website: The man who wasn't John Charles Brown

We may have more in common with friends than we think we do:

Correlated genotypes in friendship networks

Full text: http://www.pnas.org/content/early/2011/01/07/1011687108.full.pdf+html

    James H. Fowlera,b,1,
    Jaime E. Settleb, and
    Nicholas A. Christakisc,d

+ Author Affiliations

    aDivision of Medical Genetics,
    bDepartment of Political Science, University of 
California at San Diego, La Jolla, CA 92093;
    cDepartment of Medicine and Department of Health 
Care Policy, Harvard Medical School, Boston, MA 02115; 
and
    dDepartment of Sociology, Faculty of Arts and 
Sciences, Harvard University, Cambridge, MA 02138

    Edited by Gene E. Robinson, University of Illinois, 
Urbana, IL, and approved December 15, 2010 
(received for review August 6, 2010)

Abstract
It is well known that humans tend to associate with other humans who have similar characteristics, but it is unclear whether this tendency has consequences for the distribution of genotypes in a population. Although geneticists have shown that populations tend to stratify genetically, this process results from geographic sorting or assortative mating, and it is unknown whether genotypes may be correlated as a consequence of nonreproductive associations or other processes. Here, we study six available genotypes from the National Longitudinal Study of Adolescent Health to test for genetic similarity between friends. Maps of the friendship networks show clustering of genotypes and, after we apply strict controls for population stratification, the results show that one genotype is positively correlated (homophily) and one genotype is negatively correlated (heterophily). A replication study in an independent sample from the Framingham Heart Study verifies that DRD2 exhibits significant homophily and that CYP2A6 exhibits significant heterophily. These unique results show that homophily and heterophily obtain on a genetic (indeed, an allelic) level, which has implications for the study of population genetics and social behavior. In particular, the results suggest that association tests should include friends’ genes and that theories of evolution should take into account the fact that humans might, in some sense, be metagenomic with respect to the humans around them.

Footnotes:

    1To whom correspondence should be addressed. E-mail: 
jhfowler@ucsd.edu.
    Author contributions: J.H.F., J.E.S., and N.A.C. 
designed research, performed research, analyzed data, 
and wrote the paper.
    The authors declare no conflict of interest.
    This article is a PNAS Direct Submission.
    This article contains supporting information online at 
www.pnas.org/lookup/suppl/doi:10.1073/pnas.1011687108/
-/DCSupplemental.

Freely available online through the PNAS open access option.

See this comment at Genetic Future by Daniel McArthur: http://www.wired.com/wiredscience/2011/01/on-sharing-genes-with-friends/