GENEALOGY DNA REPORT FOR JOSEPH PHILIP RHEIN
(McKinney and Stewart Website)
In the study of the ancient ancestry of humans, scientists focus on "haplogroups",
the classification of all humans into ancient family clans based on the unique
pattern of genetic markers called "SNPs" (single-nucleotide polymorphism) found
in their DNA. SNPs are small changes in the DNA which occur naturally over time.
Once a SNP occurs, it becomes a unique lineage marker that is passed down to all
future generations. Humans who have descended from the same ancient family
clan will share the same pattern of SNPs. Using SNPs, scientists have been able to
plot the haplogroups of all humans living today into a single phylogenetic tree of
mankind which shows how all humans are connected to each other in a complex
worldwide tree that stems from Africa over 150,000 years ago. Dozens of
haplogroups have been discovered to date, each haplogroup representing a major
branch in the phylogenetic tree of mankind.
Each haplogroup can be further refined into "subclades" (finer sub-branches of
the tree). As new SNPs are discovered, the phylogenetic tree becomes
increasingly detailed with finer branches and enhanced resolution. By testing
individuals from around the world and analyzing their precise placement in the
phylogenetic tree of mankind, scientists are attempting to piece together the
intricate puzzle of ancient human connections and migrations.
My Results
The results of my three DNA tests by Family Tree DNA ordered on December 28,
2013 follow. They are listed in order of their relevance for those who follow this
website.
Mitochondrial DNA (mtDNA)
This tests a man or woman along their direct maternal line. Known individuals in
the past five generations of my mother’s maternal (and mine) were born in the
Province of Pennsylvania in Colonial America or later in the United States. Their
forebears emigrated almost exclusively from Scotland, the north of Ireland, and
Germany. The seven are my mother, Mabel Florence McKinney (1901-1996), her
mother Rosa Linda Stewart (1868-1943), her mother Christena Hilliard (18401911), her mother Anna Maria Schick ( (1811-1869), her mother Anna Margaret
Mueller (1786-1817), her mother Susanna Lauback (1757-1837), and her mother
Margaretha Elizabeth Jansen (born 1730), my maternal 5th great-grandmother.
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My mtDNA Haplogroup is H5a1. There are three levels of matching along with the
number of matches that I have at each level.
Level
Matches
HVR1 - 52 generations about 1,300 years.
96
HVR2 – 28 generations about 700 years.
331
HVR1and2 and Coding Region – 5 generations about 125 years.
300
For the above match in each of the levels, I have the name of the individual and
his or her maternal forebear. Unfortunately the majority of these individuals do
not include any detailed information on the forebear nor do they post a GEDCOM
so I am unable generally to determine any specific relationship line.
In addition to the above I have listed these maternal forebears on several project
sites on Family Tree DNA with the following results.
German, listed in the name of my 5th great maternal grandmother, Margaretha
Elizabeth Jansen, born May 15, 1730 Danville, Province of Pennsylvania in Colonial
America. I have a direct match with Susannah Wheeler, born 1677 in Long
Compton, Warwick, Wickshire.
Ireland, I have direct matches with Almira Porter; Ellen Carol, born 1810; Mary
Manning, born 1873, County Cork, Ireland; and Keziah Campbell, born about
1755, North Carolina.
My maternal grandmother, Rosa Linda Stewart, is listed on Stewart Clan Society
of America. There are no matches.
Autosomal (atMDA)
This tests a couple for all ancestry. It covers both the maternal and paternal sides
of the family tree, so it covers all lineages. It is the combined DNA ancestry of my
father, Joseph Peter Rhein and my mother Mabel Florence McKinney and their
forebears.
It has a feature called Family Finder that includes a component called Population
Finder. It applies principal component analysis to the same autosomal data to
conduct biogeographical analysis (BGA) of the autosomal DNA. The results of this
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test provide percentages of a DNA associated with general regions or specific
ethnic groups (ex. Western Europe, Asia, Jewish, Native American, etc.). Unlike
some other testing companies, Family Tree DNA chose to strip out markers for
mendelian medical issues, mtDNA results, and Y-DNA SNP results. X-Chromosome
results are available for download, but are not used by Family Tree DNA's
matching program.
I have 555 matches, generally 2nd to 5th cousins. None of these appear to be on
my paternal side.
My mix is as follows:
British Isles 40%, Scandinavia 28%, Southern Europe 19%, Eastern Europe 6%,
Asia Minor 4%, and Central Asia 3%.
Again, the majority of these individuals do not include any detailed information
on the forebear nor do they post a GEDCOM on any of the websites so I am
unable to determine a specific relationship line. I assume they have not done a
significant amount of research on their genealogy lines and are looking for a
direct match.
Y- Chromosome (Y-DNA) Genealogy
This tests a male along his direct paternal line. It requires a male sample provider.
My initial Y-DNA Haplogroup was E-M44. This line originated in Africa or Asia over
60,000 years ago and the successor groups were later in what are now the
Balkans, Middle East and Southern France 22,000 to 18,000 years before current
time. I have indentified three individuals in Haplogroup E whose early forebear
has the same first twelve markers as my forebear but that relationship dates back
at most a few thousand years and there is no other information. The predecessor
or ancestor Haplogroups are DE the D then E1 then M96 then E-44.
The chart on the St.Clair/Sinclair web site following illustrates the movement of
Haplogroups DE, then successor D, then successor E, E1-M96, E-44, E1a1 my line.
Note the migration of the R groups principally to Europe, Scandanavia and Britain.
http://www.stclairresearch.com/images/ChartPath-F.jpg
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On July 28, 2015 I was advised by ftdna that my Halogroup was changed to EL632. I have listed my DNA results on the following projects at ftdna.
Project
Website
http://www.familytreedna.com/public/Alsace/
Alsace
Approximately 50 individuals. I am in Halogroup E with two other individuals
E-V13. Other groups are G with 1, I with 4, J with 1, Q with 1, R 1b1a2 with 8,
One individual ungrouped. R1b1a2 that include three individuals who
married a Herman, Frey, and Gross surnames married to Rheins in
Herrlisheim..
http://www.familytreedna.com/public/e1a1/default.aspx/
E1a1
This is Doug Phelps’ group.
http://www.familytreedna.com/public/frenchheritage/
French_Heritage_DNA
Germany-YDNA
Approximately 2,500 individuals. Primary group is R. Also shown
are E-M78, EL117,E-M34, E-M183, E-V13, and E-CTS6143. I am ungrouped at
E-L632.
http://www.familytreedna.com/public/germany/
Approximately 3,000 individuals, principally R, G and I. E-M34,
E-M35, E-M78, E-M81, E-V13, and E-V22 are also represented.
I am ungroped at E-L632.
http://www.familytreedna.com/public/HaplogroupE1andE/
E1a-(M33, M132)
Approximately 96 individuals. There are four of us from your group currently listed.
http://www.worldfamilies.net/surnames/rinehart/
Rinehart and Rhein
Approximately 35 individuals. Majority in R1b. I am in E along with
Two other individuals.
Switzerland
http://www.familytreedna.com/public/switzerland/
Approximately 200 individuals, principally R. I am ungrouped at E-L632.

****
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Project
Website
Also enclosed is a listing of E-L632 from your group.
Joe Rhein
July 31, 2015
I am also registered on Clan Stewart Society. Over 750 individuals listed. I am in
Group E1b – Haplogroup E1b1b1 Unassigned.
https://www.familytreedna.com/public/Stewart/default.aspx?section=yresults
I am not registered on the site for Greece. They show eight individuals with E;
L117 (3), M78 (2), L542 (2), and DE-M145.
Recently in Ergolding, Bavaria, Germany, not too far Southeast of Alsace, an
archaeological dig by the Bavarian State Department of Monuments and Sights
revealed more than 440 graves. So far, DNA analysis of six of the men of early
adult age was performed.
“These six men were buried together in a wooden chamber, a grave identified as
#244. The individuals were marked as 244A to 244F. Individuals found in the
western part of the chamber (244A, 244B, and 244C) lied straight on the back,
body-by-body, and all 3 men were buried with swords, spears, shields, and spurs,
like heavily armored mounted warriors. Historic value of the artifacts found in the
grave 244 makes this place one of the richest Bavarian burial sites from the lateMerowig period. Grave 244 dates to the period around 670 AD. The eastern part
of the burial chamber with the individuals 244D, 244E, and 244F was robbed and
therefore no valuable artifacts were found. Of the six skeletons tested, four were
of the R1b Haplogroup. Two were of the G2a Haplogroup. It’s unusual to find this
later group in this part of Europe, but it may match up with the Sarmatians, of
Persian nomadic tribes, which moved gradually from the Caspian plains to Eastern
Europe. They lived on the plains between the Black Sea and the Caspian Sea,
north of the Caucasus. These people of the Steppes, with their horsemanship,
armor, and female warriors, were early precursors of the knights of the middle
ages. This seems to fit with the fact that three of these skeletons were found with
swords, spears, shields, and spurs. The archaeologists said they appeared to be
heavily armored warriors.”
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Twenty four Y-chromosome haplotypes were obtained for most of the men. The
estimated haplogroup for four of the men is R1b and for the other two is G2a. I
matched seven of the markers for the Rb1 men and six for the G2a men, not
enough for anything conclusive. I mention this as an example of the sort of
investigative work that needs to be done in pursuing ones Y-DNA.
The R1b Haplogroup is the dominant paternal lineage marker of Western Europe.
It is the dominate marker for the Y-DNA German Project that contains
approximately 3,000 individuals. G2a is also frequently listed. There are a
number of males with the E haplogroup (including mine) also listed but no
matches.
It is the dominate marker for the Y-DNA Alsace Project that contains 28
individuals. I am listed with one other individual in the E haplogroup but no
matches.
A number of the forebears of Germans and French that have been Y-DNA tested
appear to have left Africa going farther North to Persia, then later to what is now
present day Kazakhstan and later to Europe; the Visigoths, the Alemanni, the
Huns, the Anglo(Angles)-Saxon Invaders, etc. A number later went to Scandinavia,
the Vikings, following the end of the Ice Age some 18,000 to 8,000 years before
current time. And, there are those who came to Gaul and to Britain with the
Roman Legions, some remaining there.
Some Limited Background On My Paternal Forebears
I am the 8th great-grandson of Johann Gaspard Rhein, born 1595 in low Alsace in
the jurisdiction of Hannau-Lichtenberg, the House of Hesse-Darmstadt, the Holy
Roman Empire, later Bas-Rhin, France, later Alsace-Lorraine, Germany, and again
later Bas-Rhin, France. My grandfather, Joseph Rhein, born 1866 in Herrlisheim,
Alsace-Lorraine, immigrated to the United States in 1890 following his military
service in the German Army. On the basis of the research I have done over the
past 45 years (none of it resulting from DNA testing) my grandfather appears to
be the only male descendant of Johann Gaspard Rhein that immigrated to the
United States. I have been unable to locate a living male descendant of Johann
Gaspard Rhein in Europe.
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I have a paternal web site at
http://www.rheinandlaeng.net/index3.html that contains 1,178 individuals –
there are no living persons listed on the site.
Some of the early settlers in Herrlisheim, low Alace may have been there in the
year 743 AD when it was conveyed to the Abbey of Wissembourg under the
name of Hariolfesvilla, the farm of Hariolf (Harold). In 1251, the village is the
property of the Counts of Oetigen, landowners of low Alsace who ceded it to
the lords of Lichtenberg in 1332. In 1480 with the death of Jacques de
Lichtenberg the heritage is divided between Phillipe de Hanau and Simon
Wecker the Count of Two-Bridge-Biche. The village is incorporated in 1570 with
the property of Hanau-Lichtenberg with the extinction of Two-Bridge-Biche. On
September 17, 1570, Phillipe IV of Hanau-Lichtenberg, one of the largest
jurisdictions in low Alsace, orders the prohibition of Mass and imposes
Protestant religion in the area. This was known as "cujus regio, ejus religio"
("whose religion, his religion"); that is the religion of the prince is the religion
of the land. The former Roman Catholic church buildings and benefices were
taken over by Protestant Churches. Subsequent to 1570, Hanau-Lichtenberg
became a part of the house of Hesse-Darmstadt. In December 1621 and
January 1622 during the Thirty Years War, Mansfeld's mercenaries raze the
area and the inhabitants of Herrlisheim and Drusenheim take refuge in tents
on the islands of the Rhein River. In the year 1681, Herrlisheim was converted
by force from Protestantism to Catholicism. Herrlisheim lies on a fertile plain
between the Vosges and the Rhine River.
I have 11 great (plus) grandfathers in Alsace whose male descendant married a
female descendant of Johann Gaspard Rhein so my y-DNA or mtDNA testing is not
applicable for these lines.
Some background on the area now known as the Balkans.
Archaeological evidence indicates that the area in what is now the Balkans was
populated well before the Neolithic Period (New Stone Age; about 10,000 years
ago). At the dawn of recorded history, two Indo-European peoples dominated the
area: the Illyrians to the west and the Thracians to the east of the great historical
divide defined by the Morava and Vardar river valleys. The Thracians were
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advanced in metalworking and in horsemanship. They intermingled with
the Greeks and gave them the Dionysian and Orphean cults, which later became
so important in classical Greek literature. The Illyrians were more exclusive, their
mountainous terrain keeping them separate from the Greeks and Thracians.
Thracian society was tribal in structure, with little inclination toward political
cohesion. In what was to become a persistent phenomenon in Balkan history,
unity was brought about mostly by external pressure. The Persian invasions of the
6th and 5th centuries BCE brought the Thracian tribes together in the Odrysian
kingdom, which fell under Macedonian influence in the 4th century BCE. The
Illyrians, ethnically akin to the Thracians, originally inhabited a large area from the
Istrian peninsula to northern Greece and as far inland as the Morava River. During
the 4th century BCE they were pushed southward by Celtic invasions, and
thereafter their territory did not extend much farther north than the Drin River.
Illyrian society, like that of the Thracians, was organized around tribal groups who
often fought wars with one another and with outsiders. Under the Celtic threat
they established a coherent political entity, but this too was destroyed by
Macedonia. Thereafter the Illyrians were known mainly as pirates who disturbed
the trade of many Greek settlements on the Adriatic coast. The Romans were also
affected and took police action, annexing much of Illyrian territory in the early 3rd
century BCE. An Illyrian kingdom based in modern-day Shkodër, Albania, remained
an important factor until its liquidation by Roman armies in 168 BCE.
The Romans were different from other major conquerors of the Balkans in that
they first arrived in the west. Later attacks were launched from the southeast as
well, so that by the 1st century CE the entire peninsula was under Roman
control. At the height of Roman power, the Balkan peoples were the most
united of any time in their history, with a common legal system, a single
ultimate arbiter of political power, and absolute military security. In addition, a
vibrant commerce was conducted along the Via Egnatia, a great east-west land
route that led from Dyrrhachium (modernDurrës, Albania) through Macedonia
to Thessalonica (modern Thessaloníki, Greece) and on to Thrace. The
northwestern part of the peninsula, including Dalmatia along the Adriatic coast
as well asPannonia around the Danube and Sava rivers, became the province
of Illyricum. What is now eastern Serbia was incorporated into Moesia, which
reached farther eastward between the Balkan Mountains and the Danube all
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the way to the Black Sea. The southeastern part of the peninsula was ruled
as Thrace, and the southern part was brought into Macedonia.
The Romans largely regarded the Danube River as their northern frontier, but in
the 2nd and 3rd centuries their authority was extended northward into Dacia, in
what is now western Romania. Dacia had been the home of a people closely
related to the Thracians. The Dacians had suffered invasion by a number of
peoples, including the Scythians, a mysterious people probably of Iranian origin
who were absorbed into the resident population. In the 3rd century BCE they
managed to contain Macedonian pressure from the south, but in later years they
were much less able to fend off Celtic invaders from the northwest. By the 1st
century CE a substantial Dacian state extended as far west as Moravia and
threatened Roman command of the Danube in the Balkans. The extension of the
Dacian state and Dacian raids across the river into Moesia prompted the
emperor Trajan in the first decade of the 2nd century to march into Dacia,
obliterate the Dacian state and Dacian society, and establish a Roman colony that
lasted until barbarian incursions forced a withdrawal back across the Danube
beginning in 271.
Christendom
The abandonment of Dacia in the second half of the 3rd century was a symptom
of Rome’s decline, leading to major changes in the 4th century. In 330 the
imperial capital was moved to Byzantium, so that any tribe intent on attacking the
seat of Roman power and opulence would thenceforth move through the Balkans
rather than into Italy. In 391 Christianity became the official religion, and in 395
the empire was divided in two. The dividing line ran through the Balkans: Illyricum
went to the western sector under Rome; the remainder went to the eastern half
and was ruled from Byzantium (by this time named Constantinople). This deep
and long-lasting division did little to alleviate the barbarian incursions of the
times. The 5th century saw devastation by, among others, the Alani, the Goths,
and the Huns. Most of these invaders soon left or were assimilated, but such was
not to be the case with the Slavs, who first arrived in the 6th century.
The Slavs were settlers and cultivators rather than plunderers and within 100
years had become a powerful factor in the region. They separated into four main
groups: Slovenes, Croats, Serbs, and Bulgarians (the last being a Turkic tribe,
the Bulgars, that was eventually absorbed by Slavs who had already settled in the
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eastern Balkans). Although in 681 the Bulgars established their own state, the
Slavs acknowledged the suzerainty of the emperor in Constantinople.
In the second half of the 9th century, Christianity was adopted by the Bulgarians
and the Serbs, both of whom chose the Byzantine rather than Roman variant of
the new religion. To the north of the Danube, the Romanians, though not Slav,
made the same choice, while the Croats, together with most of the rest of what
had been Rome’s section of the divided empire, became part of the western
Christian community. The Albanians, isolated behind their mountain chains, were
not much affected by either branch of Christianity. The divisions and competition
between Rome and Constantinople intensified, with the two communities
separating irrevocably in 1054. The dividing line of 395 was thus reinforced: the
Croats and Slovenes became an integral part of Roman Catholic Europe, with its
Latin script and culture, and the Serbs, Bulgarians, and Romanians joined the
Greeks in their allegiance to Eastern Orthodoxy.
Conclusion
Of the many genealogy DNA software packages on the market today Family Tree
DNA, in my view, has the most features and functionally and offers access to
many surname and geographically project sites. I encourage those of you on the
list to do some research on the benefits and limitations before ordering any DNA
testing to make sure it meets your needs. The price differential can be significant.
Genealogy DNA has come a long way but it is not quite the exact science that it
would appear. It is an evolving work. The hundreds of thousands of individuals
who have been tested have overwhelmed the limited resources of companies in
this field who analyze and categorize the results. The results should improve in
the coming years as the technology gets better.
For those of you who may be interested, I use Family Tree Maker software,
currently year 2014, Version 22.0.0.120. I have 9,954 individuals listed, including
the family of my daughter-in-law and the family of my son-in-law.
I am pleased to report that Kevin W. Stewart, President of The Clan Stewart
Society in America and a descendant of our Lt. William Stewart has been DNA
tested and will be reporting his result to me shortly. Also, Alec Stewart a
descendant of Lt. William Stewart is to be DNA tested and will be reporting his
results. Kevin and Alec were born in Clarion County, Pennsylvania and the three of
us are cousins.
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There are four Stewart sites with a total of 1,345 individuals on Family Tree DNA.
There is at least one listing for a descendant of each of the following three
individuals.
John Stewart of Jedworth and DeForesta (1350-1402) my 16th greatgrandfather.
Sir John Stewart of Bonkyl (killed at the battle of Falkirk, July 22, 1298) my
19th great-grandfather.
Walter Fitz Alan (1106-1177) the First High Steward of Scotland, my 23rd
great-grandfather, and beyond.
I am hopeful Kevin’s and Alec’s test results will confirm our male lineage as
reported on the McKinney and Stewart website.
Joe Rhein
Sarasota, Florida
July 31, 2014
Updated July 31, 2015
Addendum
Attached is an excellent article on Y-DNA testing.
http://www.isogg.org/wiki/Y-DNA_SNP_testing_chart
Following are some observations of the Big Y test that I recently completed. This
article is by Ray Banks.
Each male has Y-DNA. It is composed of 30 million sites. The DNA exists as double
strands with a molecule at each end of the strand. Every now and then the two
strands unwind to be part of some process. The strand and the two compounds
at either end are called a base pair. These molecules vary in 12 combinations and
each component is designated A, C, G or T representing the first name of the
molecule.
For the type of DNA testing in which we are interested, they force the DNA to
unravel. They then add enzymes that make numerous copies of everything. Then
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they try to get the fragments of DNA to align to known sequences of molecules. A
molecule like this is called just a base pair once it is separated from the other
molecule. And they try to make a series of about 100 adjacent base pairs to align
to a known sequence. Helping in this process is that about only 1 of 20
million stable base pairs will be replaced by another each generation. However,
there are also lots of sections where the same base pair will be repeated multiple
times. This means that sometimes a section with lots of repeats of the same base
pair will look somewhat similar to multiple parts of Y-DNA and multiple different
fragments will align with a reference section.
And I mentioned 20 million sites are stable. There are about 10 million useless,
unstable sites which apparently do not serve any purpose and suffer repeated
mutations.
One of the most striking problem areas involves the sites numbered 11 million to
12 million. These are so bad that they never report the results. They are in the
centromere where a short arm of the chromosome joins.
At the beginning of the chromosome in numbers 1 through 2.6 million is a poorly
understood area that is never reported. At the huge end of the chromosome is
another section that is almost never reported from about 28 million to the end.
In between there are problem areas. The mentioned area around the centromere
can be problematic. The area from 24 million to 28.4 million comprise
palindromes, as are several much smaller sections. These palindromes can be
complicated to explain. But often there will be multiple components. These
palindromes also tend to be far less stable than other parts of the Y-DNA. They
can't be tested in many types of tests. In the very first scientific YDNA work,
multiple mutations in the 26 million palindrome area were created as tests and
used to define branches of the Y tree. We have had to retire almost all of these
(such as P16, P18, P20) because close relatives were getting varying results.
So in my analysis of your Big Y, I no longer include any comments for the sections
reported by Family Tree DNA which fall within most of the palindromes.
One final section of immense problems is the one from 22.21 to 24.45 million.
The other companies that do Y analyses have typically reported everything in this
section as useless. This is the final section with underlying problems for us. It is
not clear why Family Tree DNA chose to report this section to you, but it often
contains almost half their reported items. Quite often most customers will have a
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positive reading at the same sites in this section over and over because it is so
unstable. I have stopped making comments on this section as no use can be
made of it. But they have also included this section when doing matching
analyses. And because of this, half of the men who show matches to their Big Y at
Family Tree do not have the man who is truly nearest to them listed as the
nearest match.
The Analysis
When Family Tree DNA reports your results, you will find three sections. The first
section is titled Known SNP mutations. We are currently aware of about 110,000
shared SNPs which have names. Family Tree reports only a small percentage of
the truly known SNPs in this section. In almost all cases, we are anyway only
interested in one or two of these that will identify your most precise
categorization. In some cases, the SNPs best categorizing you will not be in this
section
The second section is titled Novel Variants, meaning new mutations not seen
before. This is not a good title. For the great bulk of customers, we are already
aware of many, many of these. Where there is already a named SNP
representing a site, I will list this in column E of your results analysis. These
named SNPs occurred earlier than your most recent branch and are shared by lots
more men.
Also in the Novel Variants section are lots of items that are actually useless. This is
because Family Tree DNA does not compare your results with all the men in the
database. These useless items are seen in multiple haplogroups and the
underlying site is unstable. It is also may be a site known to provide inconsistent
results or conflicting results. But also within the Novel Variants section are the
truly useful mutations, which I will designate as just new. These are so far unique
to you, but whenever someone else in your haplogroup shares the same
mutation, it will be the basis of a new subgroup and tree branch.
The Big Y provides results for about half the 20 million useful Y-DNA sites. So you
will actually have twice as many unique mutations than they report. It is thought
that a Y mutation in Big Y occurs about once every 150 yrs. So you can multiply
the number of your new unique mutations by 150 to see how long it has been
since you shared a common paternal ancestor with someone else who has had
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sequencing. Identifying this branching allows us to trace your ancestral
migrations as more and more men are tested.
What is a positive reading?
It is not possible to use an electron microscope to determine one by one the
results for each of the 10 million Big Y sites. The labs instead rely on software to
aggregate the info on what base pair was found at each site. In Big Y this is
attempted 50 times on average. When all 50 reads have the same result, there is
no question the man is either positive or negative. The result is compared to a
reference sample from haplogroup R to make the determination of positive or
negative.
But this whole process is not otherwise 100% clear-cut. If a man has 48 reads
saying he has C at site 14,343,888 and two that say T, it is extremely likely that the
C reading is correct. But what if there are 35 saying C and 15 saying T. To me this
should be reported as inconclusive, but the labs that do analyses have here and
there actually instead reported a false positive or false negative by not requiring a
huge majority of the reads to be one way or the other. I suspect this is due to the
software. The software is really intended for the medical community who in their
research do not want to miss the possibility of a mutation.
Your Family Tree DNA report will almost always provide enough new mutations
for future use. However, Family Tree will not report items unless they were able
to get at least 10 reads, thus over looking a mutation. Another complication is
that there may be a valid mutation present at a particular site but the alignments
muddy the picture or the software gives a mediocre score to the site. With
individual testing of the site, it may prove eventually a useful site. So the whole
process involving sequencing is very good, but not perfect.
The problem of them only reporting an item with 10 reads can be overcome by
paying up to $50 at YFull or Full Genomes Corp to have a separate analysis done
which could uncover a few more mutations. However, I have seldom needed an
additional analysis for my work, and I simply do not have time to enter alternative
data from yet another source into the master spreadsheet.
While Family Tree DNA reports all your positive results, there are only abt 800
pertinent to a haplogroup G man and abt 1200 to C & D men. Most of these
results can be predicted in advance if we can pinpoint your subgroup. But there
are results available for 10 million sites in your raw data file. It is only in the raw
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data file where we can distinguish a negative from an inconclusive from no read
at all. This data file is called a BAM file, and it is huge, often 1 gigabyte in size. At
some point, I will ask for access to this. It is also the only place in the future
where we can look up your results for a new mutation someone else has. I
commonly use the BAM file to confirm that a man within a subgroup is negative
for a new mutation found in another member of the subgroup.
My analysis.
At this point, I have analyzed the sequencing results from about 2,500 samples
with the help of others, including about 60 Big Y tests.
I am the content expert at ISOGG for haplogroups C, D, and G. I am the only
person who can approve a new subgroup on these Y trees there. This is the one
for haplogroup G
http://www.isogg.org/tree/ISOGG_HapgrpG.html
These Y trees have now been cited in over 200 publications. This is not the case,
for example, with the trees shown at Family Tree DNA, YFull, 23andMe, Britians
DNA, etc. These ISOGG trees are used by scientists frequently, and we have a few
who insist that their new mutations be included in the index before they appear
in publication. I do not know why you chose to do a Big Y test, but one of your
goals should be to have your results used to better identifying tree branching
pertinent to you and have that incorporated into the ISOGG tree.
I am also your haplogroup project administrator or co-administrator. I work
fulltime in identifying new Y-DNA branches. And in this role, I always go through
results to see what new can be identified. Presently on 11 Jan, I am 3-4s week
behind in Big Y processing. Most of the problem is related to a separate project
to provide for the first time a mega Y tree that tries to merge all the subgroups
identifying in about a dozen sources. This is a huge undertaking. But I only have 1
of the 30 haplogroups yet to do. At the top of each ISOGG page you will find a
link to my Composite Y tree.
I am also co-author of a paper with one of the most ambitious Y-trees yet
attempted.
http://biorxiv.org/content/early/2013/11/24/000802 I covered 8 haplogroups for
this. The lead author is Dr. Gregory Magoon, a graduate of M.I.T. in the United
States who does analysis for Full Genomes Corp., and the senior author is Dr.
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Andy Grierson from the University of Sheffield, a molecular biologist with a
special interest in population genetics.
My analysis is free to you. I am a volunteer with no staff.
Final Goals
There are two sets of goals for me, and I hope they will also be your goals.
The first is to improve the knowledge of which mutations comprise a subgroup.
This may also include finding the results from one subgroup for a sister subgroup.
In some cases, the subgroups are well defined, but in other cases not enough
men have provided sequencing to even figure out yet how they fit together.
The second goal is to create yet another subgroup from the SNPs that are unique
to you. For this to work, we need to have a second man fairly near to you in
marker values but not a relative. He must have at least five marker values
different at 67 markers to qualify. But once a man has 10 or more markers
different, the chances of him sharing one of your new SNPs randomly chosen
significantly diminishes and the cost of testing lots of SNPs can become quite
expensive.
ISOGG criteria requires this 5 marker values diversity in the two men validating a
new subgroup. Criteria also require that the submitted evidence involve
individual testing (the $39 test at Family Tree DNA, the $35 test at YSeq.) Big Y
and Geno 2.0 are not reliable enough to validate the new subgroup. These
individual tests use what is called Sanger sequencing and allow making sure there
is a correct alignment. Family Tree DNA will allow testing new SNPs but it has to
be a small number of them. We generally restrict such testing to obvious new
subgroups. Where we are randomly testing new unique SNPs, we have to use
YSeq. http://www.yseq.net/
YSeq will test any SNP. It is operated by persons who used to do this same type
testing at Family Tree. If the additional testing involves testing of both obvious
subgroups plus expected additional testing randomly of unique SNP, YSeq is the
first choice. We have been subsidizing this type testing mostly from donations,
and we are adding about one new subgroup a week to the ISOGG trees.
Ray Banks
dnagrouper2@gmail.com
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