Lesson 2: DNA Basics

What it looks like, who discovered it, uses and much more!

http://en.wikipedia.org/wiki/DNA

Lesson 3: Transmission

The paths Y-chromosome and mtDNA travels:

http://www.kerchner.com/y&mtdna.htm

Charles Kerchner's charts are in a concise and easy-to-understand format which clearly illustrate the transmission of DNA from parent to child.

Lesson 4: DNA Sampling

Bob Dorsey gives a detailed and humorous demonstration of how DNA is collected for sampling:

http://davedorsey.com/dna.html

Lesson 5: DNA Processing

When Family Tree DNA receives your kit, it is placed in a batch which averages about 1,000 other kits. The batch is assigned a number and then sent to the University of Arizona lab for processing.* You'll need a flash plugin to view the following FTDNA lab processing presentation:

http://www.familytreedna.com/flash/presentation1.html

Here's Relative Genetics tutorial on DNA processing:

http://www.relativegenetics.com/relativegenetics/tutorial/testing_process.htm


*PLEASE NOTE: All kits in an FTDNA batch will not return results at the same time. Tests like the mtDNA H-clade test, the 67-marker upgrade and deep SNP testing all take longer than 12-37 or mtDNA HVR1 & 2 processing.

Lesson 6: The Results

Once your results are in, many people do not know what to do next or where to go to find answers.

Basically, your DNA results are a series of numbers that derive meaning when compared to others' results. For both Y-chromosome and mtDNA you receive the names and e-mails of those you match within the database. If you upload your results to a public database, such as Y-search.org, Y-base.org, and/or Mitosearch.org, then you may find that you have matches with people who have tested at other companies than the one which you've tested with. Oftentimes, you may have to wait for the right person to test until you have a meaningful match.

Lesson 7: Mutations

As Wikipedia cites, mutations are a change in genetic material:
http://en.wikipedia.org/wiki/Mutations

While the word has a negative connotation in our society, mutations in
genetic genealogy are beneficial for identifying ancestral patterns
within haplotypes (your DNA signature). If mutations cause you to be
one, two, three, and sometimes even four off on a 37-marker match, it
is still considered a match. (The four mismatches may be caused by
another factor such as a RecLOH event, but we'll cover that later).

As Wikipedia also states, mutations can sometimes be caused by
radiation, and other mutagens. For example: Pilots may have more
mutations than average since they are exposed to atmospheric
radiation.

Lesson 8: Mismatches

As referenced in Lesson 7, two people can be off by as much as four out of 37-markers and still be a match, dependant upon various circumstances.

For example: A male may have had a RecLOH event occur in a palindromic region (palindromes are the multi-copy markers i.e.: 385a, 385b, etc.) In such a case, the RecLOH event should be given the genetic distance of one as opposed to determining that two males are off by two.

Some families may have a higher instance of mutations where it may be necessary to order more than 37 or 43 markers to reveal whether the match is a true match or becomes farther apart.

In some cases, two males will mismatch on far more than 4 markers and are thus deemed to be unrelated. If their haplogroups differ, they most definitely are unrelated.

For review: "Interpreting Genetic Distance within Surname Projects"
http://www.familytreedna.com/GDRules_37.html

Lesson 9: NPEs

Lesson 8 covered mis-matches, and mis-matches can sometimes be
caused by NPEs. "NPE" is the acronym for "Non-paternal Event" which
is a term used to apply to events that occurred in the past that may
have been due to illegitimacy, adoption, fostering, etc. The name
is actually a misnomer because no one has a "non-paternal" event in
that everyone has a father. At the FTDNA Conference, Roberta Estes
shared that she uses the term "undocumented adoptions" instead of
using NPE, but unfortunately, NPE is a widespread term and probably
here to stay.

NPEs are often the cause of mis-matches. Sometimes, the NPE is
known about ahead of time, and sometimes it is not.
http://www.isogg.org/npe.htm

Family members often question whether or not they are still family
when an NPE has been revealed. An excellent essay on the topic has
been compiled by the late Don Dickason:
Familial and Genetic Descendancy; Conflict or Complement?
http://www.isogg.org/fgd.htm

Lesson 10: Y-chromosome Terminology

Since we're still mostly in the realm of the Y-chromosome, thought
it would be good to cover some terminology.

Marker - A specific place on a chromosome with two or more forms,
called alleles, the inheritance of which can be followed from one
generation to the next. In genetic genealogy, this refers to non-
coding Y-chromosome DNA. Numbers designate the individual DNA
segments. Example: 393=13. This means at marker #393, your allele
value is 13.

DYS - Acronym for DNA Y-chromosome Segment - The assigned number of
a marker on a segment of the Y-chromosome. Example: DYS# 393

The acronym 'YSTR' stands for Y-chromosome Short Tandem Repeat. The
number of times the sequence of bases repeat that determines the
value of the marker. Example: Thirteen repeats of the same bases
equals a value of '13'.

You will also sometimes see it referred to as just 'STR'. The whole
string of numbers is known as a 'haplotype' - some people also refer
to this as a 'signature' or 'DNA signature'.

People often confuse a 'haplotype' with a 'haplogroup' and many do
not know the difference. Even for myself, it was like a lightbulb
going on when I learned the difference. A 'haplogroup' is a group
of similar haplotypes that share a common ancestor with a SNP
mutation.

Read Charles Kerchner's excellent "Haplotype vs. haplogroup":
http://www.kerchner.com/haplogroupvshaplotype.htm

Definitions source:
http://www.isogg.org/glossary.htm

Lesson 11: Haplogroups & SNPs

From the DNA-NEWBIE Glossary:
http://www.isogg.org/glossary.htm

Haplogroup - A group of similar haplotypes that share a common
ancestor with a SNP mutation. Because a haplogroup consists of
similar haplotypes, this is what makes it possible to predict a
haplogroup. A SNP test confirms a haplogroup. Haplogroups are
assigned letters of the alphabet, and refinements consist of
additional number and letter combinations, Example: R1b1. Y-
chromosome and mitochondrial DNA haplogroups have different
haplogroup designations. Haplogroups pertain to your deep ancestral
origins dating back thousands of years.

SNP - (pronounced SNIP) - Acronym for Single Nucleotide
Polymorphism. A SNP test confirms your haplogroup by determining if
a SNP has mutated from its derived or ancestral state. A SNP is
usually found on a different area of the Y-chromosome than where the
YSTR markers are. Sometimes, a SNP may cause a null result on a
marker.

Katherine's comments: Several DNA testing companies offer free
haplogroup predictions. They are able to do this by comparing your
haplotype to haplotypes in either a scientific database, proprietary
database or both.

As defined above, haplogroups are your deep ancestral origins on
just one direct line. While some might consider it a drawback to
only be able to confirm ancestry on one direct line, the benefit of
this is that with SNP confirmed results, the results are
unambiguous. At the 3rd International Conference on Genetic
Genealogy, Family Tree DNA debuted a new "SNP Assurance Program":
http://www.familytreedna.com/SNP_assurance.html

Family Tree DNA already SNP confirms ALL mtDNA results so further
SNP confirmation is not required. (we'll go into this further in the
mtDNA Educational Component)

At this moment in time, haplogroup confirmation tests do not yet go
very far out on the phylogenetic tree, some of the furthest I've
seen is in the R1b haplogroup, i.e.: R1b1c7
To view an updated phylogenetic haplogroup tree, visit the 2006
ISOGG Tree at:
http://isogg.org/tree/

Lesson 12: Whit's Predictor

Lesson 11 covered haplogroups and SNPs and an important tool that should be mentioned at this point is "Whit's Predictor": https://home.comcast.net/~whitathey/predictorinstr.htm 

Whit Athey compiled the "Y-Haplogroup Predictor" as a tool to utilize by entering a haplotype which yields percentages for the most likely haplogroups. Try it out! (If you have dial-up internet, you might need to walk away while it loads because it can take a long time over a dial up connection) Enjoy!

Lesson 13:  mtDNA Tutorial

From the DNA-NEWBIE Glossary: Mitochondrial DNA - Energy releasing organelles located in the cytoplasm of cells, which contain their own DNA.  Mitochondrial DNA is passed from mother to child, but only females continue to pass on their maternal mitochondria to their children. http://www.isogg.org/glossary.htm 

Mitochondrial DNA is passed from a mother to her children, but only her daughters will pass on her mitochondrial DNA to their children. 

More: What is mitochondrial DNA? http://ghr.nlm.nih.gov/handbook/basics/mtdna 

What mitochondrial DNA looks like: http://ghr.nlm.nih.gov/handbook/illustrations/cellparts?show=cellmitochondria

Family Tree DNA has compiled a tutorial on mtDNA that might was well be called "Everything You Ever Wanted To Know About mtDNA":

http://www.familytreedna.com/mtDNA_tutorial.html Ok...well, "almost" everything you want to know...it doesn't cover scenarios for using mtDNA with genealogy, but that's tomorrow's DNA- NEWBIE Educational Component.

Lesson 14: mtDNA Tree

Mitochondrial DNA (mtDNA) is most often associated with deep ancestral origins since it mutates (changes) very slowly over time.  Like Y-DNA haplogroups, mtDNA also has haplogroup designations.  However, the letters for Y-DNA and mtDNA haplogroup designations do not correspond to each other.  A 'K' in Y-DNA does not have the same ancestral origins as a 'K' in mtDNA. 

Sometimes, you will see mtDNA haplogroups referred to with names, like 'Katrine' for 'K'.  This naming convention originated in Bryan Sykes' book, "The Seven Daughters of Eve". 

mtDNA haplogroup H is the most common mtDNA haplogroup found in Europe. mtDNA haplogroup tree: http://www.stats.gla.ac.uk/~vincent/images/skeleton07-08-02.jpg

Lesson 15: mtDNA & Genealogy - Part 1

Because our female ancestors did not keep their surnames, and we are fortunate if their first names, let alone their last names were recorded at all, mtDNA matches are not as easily revealed as Y-DNA matches.  Another contributing factor may be that mtDNA mutates (changes) much more slowly than Y-DNA. 

So how can we use mtDNA for genealogical purposes? 

One of the best and most successful ways to use mtDNA is in the manner that Bill Hurst used it with the Kelly Sisters.  He tested two known descendants, and concluded that the match confirmed indirect census and other records showing that Martha Kelly and Catherine Kelly were sisters and that their mother was Elizabeth Cummins Kelly. More on the Kelly Sisters match: http://freepages.genealogy.rootsweb.com/~wrhurst/dna/hurstdnasuccessstories.htm

Lesson 16: mtDNA & Genealogy - Part 2

Like Bill Hurst, another family recently used mtDNA to prove whether two lines were related. But this situation occurred much more recently in time and there was an adoption involved. The following mtDNA success story has been posted on the main ISOGG site courtesy of David Pitts, the Pitts Surname DNA Project Administrator:

"Emma's mother was unwed and barely 18 years old. When Emma was born, an old preacher abducted her and raised her as his own. He probably thought he was doing the right thing and later he claimed to have legally adopted her (e.g. 1930 census). Emma was raised with the preacher's surname and she never knew her real mother's name. Emma's daughter recently started to add some genealogical evidence such as census records to the family stories so that she could present an iron clad story of Emma's ancestry to her before she died. Despite her best efforts there was always some doubt that she had the right family. Emma's daughter did some research on the
web and discovered that mtDNA might offer a tool to solve this puzzle once and for all. Using her own mtDNA and mtDNA from Emma's presumed Aunt Oleta (HVR1 & HVR2), she found an exact match, thus confirming the paper trail!"

Lesson 17: mtDNA & Genealogy - Part 3

mtDNA results can also point someone in the direction they need to go in to research their line. This is what happened with Marie Rundquist when she tested through the National Geographic Genographic Project:

"I have been tested in the National Geographic Genographic project; my results have been transferred to Family Tree DNA. I am a member of Haplogroup A. My lineage is French/Cajun (through my mother's line); my Ancestral/Native routes are found in Nova Scotia, where a French settler, Rene Rimbault, married an Amerindian woman, known only as Anne Marie. It is through this union, that occurred in the mid-1600s, that my Native American and French lineage can be originally traced. I had no knowledge of my Amerindian lineage before participating in the Genographic project; I was totally knocked out of my chair when I read the results on line. Mind you, I NEVER knew anything about the female line of my family until my mtDNA results came in as "Native American". This revelation caused my dad (and others) to get their DNA tested. I've learned alot about my background since; and thankfully have met other folk who have helped me solve all these mysteries in my own family's background."

Read more about Marie's story at:
http://www.frenchdna.org/findingannemarie.html


Lesson 18: mtDNA & Genealogy - Part 4

A case where mtDNA was used to find a lost paper trail (much in the same way that we use Y-DNA) occurred as a result of Linda Thompson Jonas' watchful eye, good memory, and having the information available that she needed. Linda is the Project Administrator of the U5 Haplogroup Project and she has people submit their pedigrees. She noticed a match which had similar geographic origins and with a little research, was able to take one woman's line back another 150 years! The full story appears here:
http://www.isogg.org/successstories.htm

Haplogroup projects have varied and diverse goals. The haplogroup H project is another one that also posts pedigrees. For a complete list of mtDNA haplogroup projects, visit:
http://www.worldfamilies.net/mtDNA.htm

PLEASE NOTE: You need to have tested prior to know what your haplogroup is before you join a haplogroup project.

Lesson 19: Famous mtDNA

When your mtDNA matches someone famous, that does not mean that you are necessarily descended from them (especially a male since males do not pass their mother's mtDNA on to their children) but it does mean that you do share a common ancestor with them.

Click here to see if you have a famous genetic cousin:

http://www.isogg.org/famoushg.htm

Lesson 20: Famous DNA

As just recently appeared in the news, DNA extracted from remains attributed to Joan of Arc might turn out not belonging to the famous French saint after all.

Is there a famous (or infamous) person on the following site that YOU share a common ancestor with?
http://isogg.org/famousdna.htm

(Remember - haplogroup letter designations do not correspond between each other - an mtDNA K is not the same as a Y-DNA K)

Lesson 21: Famous DNA Extraction

Typically, when DNA was (is?) extracted from old remains, it usually
meant having to destroy part of the bones to be able to extract viable
DNA. Bryan Sykes details this in "Seven Daughters of Eve" where he
first drills into Cheddar Man's toe and then later a tooth. But new
technology may mean less invasive and destructive means:

'Better' DNA out of fossil bones
http://news.bbc.co.uk/1/hi/sci/tech/4260334.stm

Even though hair is often the first thought of source for DNA, it
rarely turns out to be usable since it is so easily contaminated. One
success story involving DNA extraction from hair is in the case of
Marie Antoinette. As technology continues to advance, more successful
methods for extracting DNA from hair will be developed, see:

Ancient Hair Gives Up DNA Secrets
http://www.abc.net.au/science/news/ancient/AncientRepublish_1135104.htm

Began at the suggestion of Tom Howle on 18 Oct 2006 on the DNA-NEWBIE Yahoo Group and mailing list.
Compiled by K. Borges
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