Saturday, April 28, 2012

DNA Analysis of Neolithic Europeans

DNA Analysis of Neolithic Europeans

Science Magazine
April 27, 2012

Archeologists and anthropologists have analyzed ancient DNA in an attempt to correlate DNA samples with geographic locations in Neolithic times. Friday's issue of Science Magazine has four autosomal results of Neolithic Europeans:

 - 3 hunter-gatherers excavated, whose distinct genetic signature is most similar to that of extant northern Europeans.

 - 1 farmer excavated in Scandinavia (Sweden) is genetically most similar to extant southern Europeans

The 3 hunter gatherer autosomal samples were excavated from burial grounds on the island of Gotland, Sweden. Associated remains have been dated to 5300-4400 years ago, or 2400 to 3300 B.C.

The one farmer has been associated with the Pitted Ware Culture were most similar to the DNA sequences of people from Finland. These remains were carbon dated dated to 4,921 ± 50 years ago, or about 3,000 BC.

Apparently, no Y-DNA haplotype group was published. But this does sound a lot like I1 and R1b. Or, R1a and R1b. If I were to guess, it would be that the three hunter-gatherers should be I1, and the one farmer to be R1b. But, Dienekes cautions that the three hunter-gatherer contemporaries "were outside the range of modern variation."

Denekes writes:

"We now have two ancient autosomal DNA sampling locations, and both turned up unexpected results. The Iceman, a Copper Age inhabitant of the Alps resembled modern Sardinians. A Megalithic Swedish farmer resembled Southern Europeans, while his hunter-gatherer contemporaries were outside the range of modern variation. These results should give us caution about the identity of past populations elsewhere.

As I have argued elsewhere, the past seems to have been much more dynamic than many had suspected..."

  (end quote)

In simplist terms, scientists have expected farmers to follow hunter-gatherers, and not the other way around. To view the article and read Deniekes Blog, follow the links below.

Science Magazine  (behind a pay-to-view firewall):

"Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe"

Pontus Skoglund, Helena Malmström, Maanasa Raghavan, Jan Storå, Per Hall, Eske Willerslev, M. Thomas P. Gilbert, Anders Götherström1, Mattias Jakobsson


The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.

See also Dienekes Blog:

"A first look at the DNA of Neolithic inhabitants from Sweden"

"Ancient DNA from Neolithic Sweden (Skoglund et al. 2012)"

                                                        To comment, click on the title and scroll to the bottom.

Ancient Migrations and the Journal of Genetic Genealogy

Journal of Genetic Genealogy

April, 2012

A Fall, 2011 issue of the Journal of Genetic Genealogy has been posted:


O.K., I know that the header says "Fall, 2011" and this is Spring of 2012. But the issue was released on or about April 24th. That may be due to the lack of an Editor, as the former editor Blaine Bettinger, resigned because of employment and family commitments.

The Editorial Board is actively seeking a new Editor.

In this issue:


"Satiable Curiosity"
Identity Crisis: Identical by State or Identical by Descent?
by Ann Turner

A column by Ann Turner, this issue deals with autosomal analysis, such as what you might see with 23andMe or FTDNA's "Family Finder" product. Her story explains the analysis of short segments, and attempts to evaluate if you can use them to determine recent relationships.
The column gives an example of how to use David Pike's Utility for this.  

See the footnotes to obtain this article as a PDF file.

Review Article:

"Melungeons, A Multi-Ethnic Population"
Roberta J. Estes, Jack H. Goins, Penny Ferguson, Janet Lewis Crain


"Melungeon is a term applied historically to a group of persons, probably multiethnic, found primarily in Hawkins and Hancock Counties, Tennessee, and in adjoining southern Lee County, Virginia. In this article we define the Melungeon population study group, then review the evidence from historical sources and DNA testing--Y-chromosome, mitochondrial DNA, and autosomal DNA--to gain insight into the origin of this mysterious group."

"On the Structure and Age of mtDNA Haplogroup JT--A Phylogenetic Tour"
J. J. Logan

Analyzed the clade structure of Haplogroup JT and from it derived estimates for the ages of the various subclades. From the article:

"The coalescence age of 49.6 kya as computed here for Haplogroups J and T is very comparable to the age of the differentiation that was said to have taken place in western India, in the region of the Fertile Crescent or in the migration path between them. It is important to emphasize that this is well before the appearance of modern humans in Europe...."

"...The age of J and T and their first order divisions suggest that migration into Europe was
occurring well before introduction of agriculture. Currently available genetic alone data does not
permit a definitive determination of the geographic location of the clades."

There is a nice Glossary at the bottom for folks not familiar with mtDNA analysis.


"The Evolution of the Gordon Surname: New Insight From Y-DNA Correlations and Genealogical Pedigrees"
Tei A. Gordon and William E. Howard III


"Surnames can be grouped into families by two methods: (1) matching Y-DNA marker haplotypes assisted by pedigree information, and (2) using correlation techniques. Both methods, applied independently, yield remarkably similar results, with the correlation technique having a slight advantage in determining the members of family groups and clusters. Traditional and correlation techniques produce similar results, with similar uncertainties, when estimating the time at which the most recent ancestor of a pair of testees lived if they are within the genealogically interesting period within about 1000 years. The correlation technique has a decided advantage when times to the most recent common ancestor of a family group, the most recent common ancestor of separate family groups, and the most recent common ancestor of families within separate haplogroups are estimated. Correlation techniques and genealogical pedigrees, working together, are used to explore the history and evolution of surname groups as well as the haplogroups of which they are a part. Totally new information that shows remarkable relationships among pedigrees, cluster and subcluster membership, geographical location, and their evolution has become apparent through this study. The appearance of surname subclusters within a surname cluster can indicate a strong, confirmable tie to pedigrees when they are available for members of a subcluster. We have uncovered correlations between recent historical activity and the formation of subclusters. The times when Gordon family clusters first appeared, and when the most recent common ancestors of Gordon interclusters lived, are compared with the chronology of the Gordon surname and events in European and Scottish history to provide additional insight into the history of the Gordon surname and possible origins from 2500 BCE to the present. The earliest most recent common Gordon ancestors who were located in pairs of different haplogroups date to about 17,500 BCE, just after the European glaciers in the most recent ice age began to recede.

In the R1b1 haplogroup, the ISOGG time estimates, the RCC time scale, the Y-DNA evidence and our results are consistent with an origin of the Gordon surname in areas near modern Turkey and Greece. Comparison of the ISOGG dates with those determined using the RCC time scale shows good agreement and no inconsistency between the RCC- and ISOGG-derived estimates. 

The times derived from the RCC matrix for the early migrations of the I1 haplogroup into the British Isles from Scandinavia and from Western Europe agree well with the history of the area derived from archaeological excavations, genetics and anthropologic studies."


"Dating Y-DNA Haplotypes on a Phylogenetic Tree: Tying the Genealogy of Pedigrees and Surname Clusters into Genetic Time Scale"
William E. Howard III and Frederic R. Schwab


"An RCC matrix (Howard 2009a), resulting from a new correlation approach to analyze Y-DNA haplotypes, is used in conjunction with a standard Mathematica application program to produce a dated phylogenetic tree. The program displays the evolutionary relationships among all haplotypes in the matrix; it groups closely related surnames into family clusters that correlate well with genealogical pedigrees. The time scale assigned to the tree is monotonic, linear, and dates the evolutionary relationships of Y-DNA testees that may go back tens of thousands of years. This study is arguably the first to investigate the time relationships between surname Y-DNA haplotypes, pedigree- and RCC matrix-derived surname clusters and their associated phylogenetic tree. It offers a straightforward methodology and a uniform time scale that can also be used to estimate the evolutionary relationships among Y-DNA haplogroups."

If you would like to see an example of a professional treatment of surname project phylogenetic trees, this is one. This TMRCA report is a little heavy on the mathematics (using Howard's correlation technique, RCC, previously published in JoGG). They have brief graphical displays of the genealogy trees in the Gordon Project, along with the graphic displays of the mathematical results.

To give an idea of the amount of work involved, they analyze two Gordon clusters, I1 and R1b:

The Evolutionary Diagrams of the Major Gordon Surname Clusters and Interclusters in Haplogroups I1 and R1b1b2

I have to say that I was most intrigued by the correlation of the Gordon surname to "Historical Events."

A Comparison of Events in the Evolution of Gordon Clusters and Events in European and Scottish History from the Maximum of the Last Glaciation to 2500 BCE

If I read that correctly, they have the Gordon Haplotype I1 populating Norway, Sweden, and Scotland from between 7500 BC to 9500 BC.

If so, then this is in huge disagreement with the "Ancient Migrations" that I derived for I1 and R1b in the Ham Country blog articles using McGee's Utility and Y-DNA STR values to trace ancient migrations of off modal I1 and R1b:

Perhaps this JoGG article might be a statement of their disagreement with my STR geographic analysis. However, they have been careful not to correlate geographic locations with the samples. They simply list historical events next to the tree. However, the article does contrast with my ancient migration blogs because in this article, the timeline is far larger.



The Journal of Genetic Genealogy, Fall, 2011

The Gordon DNA Project

House of Gordon research

DNA processing lab
Mathematica software program:

"Ancient Migrations" that I derived for I1 and R1b in the Ham Country blog articles using McGee's Utility and Y-DNA STR values to trace ancient migrations of off modal I1 and R1b:
                                   To post a comment, click on the title and scroll to the bottom of the page.

Sunday, April 22, 2012

Greg Ham Men At Work Musician

Greg Ham
Men At Work Musician
Dies at age 58

774 ABC Melbourne 
Greg Ham was found dead in his Melbourne home on Thursday, April 19, 2012.
Member of the Australian band "Men at Work."

Mr. Ham was featured playing the flute in the hit song "Down Under," and played the saxophone in "Who Can It be Now."

Friends said he hadn't been the same since 2010, when a court ruled against his signature flute riff from the song "Down Under." In 2010 Australia's Federal Court ruled band members partly copied the flute riff from the children's folk tune "Kookaburra
Sits in the Old Gum Tree," penned more than 75 years ago.

Men At Work won the Grammy Award for Best New Artist in 1983 before disbanding in 1985.
Thanks to Kenelly Marka for posting to the Rootsweb Ham genealogy email list.

Greg Ham - Men at Work
Greg Ham, second from left. BBC News Article: 

Greg Ham in "Down Under" video VVN News:


BBC News article:

VVN / Music article:

New York Times article:

You Tube videos

                                              To post a comment, click on the title and scroll to the bottom.

Wednesday, April 11, 2012

HAM DNA Project Group Changes

HAM DNA Project

Group Changes

The HAM DNA Project has a new participant this week, Carl Hamm, kit #226942. Carl descends from Rufus HAM b. abt 1878 of Washington County, VA. Very curious history, because there is documentation on several Rufus HAM's from the area of SW Virginia during that time frame. 

The DNA suggests some connection to the Ashe County, NC/Franklin County, NC, and the Patrick County, VA HAM lines. He appears to be the closest DNA match to the Ashe County lines, in particular, the descendants of John HAM (1780-1850) of Grayson County, VA.

However, we should keep in mind that the Washington County, VA lines have not yet been fully represented in the DNA Project. You can view his results here:

I got some FaceBook messages recently about how the Groupings are done for the DNA Project. I thought I would take a moment to re-arrange the HAM DNA Groups so that they better reflect the Phylogenetic tree output. I wanted to have the groups show the output from the "kitsch" program a little bit better. Basically, the thought is that the standard scientific tools should deliver the groupings in the best way that can be determined at this time. I think most of the changes to the groups have been driven largely by those few who have tested to 111 markers, as well as by the new participants. However, in one case of the new grouping, both participants have only tested to 25 markers.

Basically, the changes that have been made are:

Group # 1 Changes

New kit #226942 was added to HAM DNA Group #1 (226942 is Rufus HAM of Washington Co., VA).
His closest matches appears to be kits 212352 (William HAM b1780 d abt 1860 Patrick County, VA) and 68140 (William HAM Sr. son John HAM (1780-1850 of Grayson Co., VA).
Clearly belongs to Group #1, but it is still not clear which line from Group #1 that Rufus would belong to.

Group # 3 Changes

Kit # 107820 has been moved from HAM DNA Group #8 to Group #3 (107820 is Jacob HAM, Sr. b. 1721 Rhine Valley, Germany).
The phylogenetic chart (of the TMRCA) wants to group him with kit #43250 (Captain Richard HAM b. est 1761 Charleston, SC; d. 1855 Pulaski County, KY).
This grouping is still tentative, as the Time to Most Recent Common Ancestor is estimated to be 1550 years ago. And, each kit has only been tested to 25 markers.
Aside from the DNA, the obvious items common to both kits are:

a) the same surname
b) both lines appear to have been in Kentucky by 1820.

The obvious differences are:

a) Jacob HAM, Sr. is known to have been born in Germany
b) Capt. Richard HAM is thought to have been from South Carolina.

I would think that an upgrade to 111 markers for these kits would help to better narrow down the time frame.

Group # 8 Changes

I have moved kit # 205092 from Group #12 to Group #8, and dissolved Group #12. Kit 205092 is Perry C. HAM born 1825 TN. Parents both born in North Carolina,
with children born in Illinois. Kit 126092 is WILLIAM HAM was born in 1821 in Georgia. Died ABT 1868 in Louisiana.
The TMRCA on the two is 900 years ago, so even this grouping is tenuous, but better than the previous grouping.
(For example, I have Valentine HAMME in a different group than DNA Group #1, largely due to the TMRCA.)

It might be worth noting that kit 126092 has only been tested to 37 markers, but 205092 has been tested to 111 markers. At 37 markers, I can't say that an upgrade to 111 markers would make a large difference in the TMRCA between the two.

What they do have in common is some matching DNA and the same surname.
Which tells me that there is a good chance that they could at least share the same city of origin.


My comment on these groups should be that Group #3 is not far in Genetic Distance from:

- Group #8,
- Group # 6 (kit #82227 Mordecai HAM of Stokes Co., NC).

- Also, the Genetic Distance for Group #8 is not far from kit #126092 in Group # 8, where I just moved kit 107820 from.

My thoughts on this is that the problems with these groups should eventually be resolved with more participants as well as an increase in the number of markers tested. This should be especially true for those who have tested to 25 markers, as 25 markers becomes unreliable for TMRCA estimates beyond about 800 years ago. I should think an upgrade in the number of markers should be important to these groups (#3, #6, and #8). Therefore, these groups could change again if more markers are tested, and as more people participate.

The Tax man is knocking at my door and taking some of my time, but I will get the phylogenetic charts updated with new kit 226942 as soon as possible.


Dean McGee's Utility output:

HAM DNA Phylogenetic charts:

                                                      To post a comment, click on the title and scroll to the bottom.