Genome

 

 

What is a genome?

A genome is an organism’s complete set of genetic instructions. Each genome contains all of the information needed to build that organism and allow it to grow and develop.

Our bodies are made up of millions of cells (100,000,000,000,000), each with their own complete set of instructions for making us, like a recipe book for the body. This set of instructions is known as our genome and is made up of DNA. Each cell in the body, for example, a skin cell or a liver cell, contains this same set of instructions:

  • The instructions in our genome are made up of DNA.
  • Within DNA is a unique chemical code that guides our growth, development and health.
  • This code is determined by the order of the four nucleotide bases that make up DNA, adenine, cytosine, guanine and thymine, A, C, G and T for short.
  • DNA has a twisted structure in the shape of a double helix.
  • Single strands of DNA are coiled up into structures called chromosomes.
  • Your chromosomes are located in the nucleus within each cell.
  • Within our chromosomes, sections of DNA are “read” together to form genes.
  • Genes control different characteristics such as eye colour and height.
  • All living things have a unique genome.
  • The human genome is made of 3.2 billion bases of DNA but other organisms have different genome sizes.

If printed out the 3.2 billion letters in your genome would:

  • Fill a stack of paperback books 200 feet (61 m) high
  • Fill 200 500-page telephone directories
  • Take a century to recite, if we recited at one letter per second for 24 hours a day
  • Extend 3,000 km (1,864 miles), that’s about the distance from London to the Canary Islands, Washington to Guatemala or from New Delhi to Hanoi.

map_dna_genome_yourgenome

Source: http://www.yourgenome.org

DNA Replication

 

 

This 3D animation shows you how DNA is copied in a cell. It shows how both strands of the DNA helix are unzipped and copied to produce two identical DNA molecules.

Source:

http://www.yourgenome.org/video/dna-replication

access 1/28/2017

 

DNA Helps Discover John Ancestors

 

 

I was introduced to genealogy by my Aunt Madeline Johns Gee  who was a well known teacher in the Williamsburg-James City County Public Schools. She pushed for integration of public schools which were segregated at the time back in the day. She was considered a pioneer, a trail blazer. At a family gathering in Greensboro, NC she introduced the family tree she created and I was really excited, never knew most of my relatives. That was 45 years ago and I began studying genealogy when it was not as popular as it is today. As I have learned about genealogy through the years I came to a startling reality. All the research and genealogy websites gear their data towards European ancestors. There is almost no research on African American genealogy and genetic genealogy. That is changing daily as genealogist work towards a common goal. I will explain more on that in one of my blogs coming soon.

I have traced my ancestors back to 1460 Herefordshire, England, with DNA testing and the help of testing results of other relatives. My research has revealed new relatives unknown before. Results of four living relatives’ DNA results indicated a relationship at 22-26 cM’s and a direct relationship to William Johns who was married to Ann Merryman. With this information I was able to discover African-Americans not recorded any place by Johns family genealogists. John Johns the son of Col. John Johns lived in the Blue Ridge Mountains (Bear Mountain) of Virginia. He had an acknowledged relationship with a Monacan Indian woman (left blank at the request of the Monocan Nation) who are now a blend of Saponis, Occaneechis, and Tutelos tribes. Most of theses tribes relocated to Pennsylvania and finally to Canada where they are today. John Johns purchased 52 acres of land on Bear Mountain. In 1833, he bought another 400 acres, and this became the settlement for Indian and African-American families related to him. In 1850, the census recorded 29 families, mostly large, related to the Bear Mountain settlement. In his will he divided his land among his sons and daughter, and five years later, at the age of 91, he died.  In 1860 the Amherst County Clerk’s Office recorded, among the names of free persons of color, the Monacan surnames of Beverly, Branham, Johns, Pinn and Terry. I have all fourteen names of African-Americans and Native American Johns who lived together and married.

The Virginia legislature passed a Race Law in 1823, which declared that any child of an Indian and any descendent of a Negro, up to the great-grandchild, would be counted as a mulatto. Virginia passed the Racial Integrity Law in 1924, which prohibited intermarriage between those considered white and those having any mixture of colored blood more than one-sixteenth. Many community settlers left the state during this time, because they were no longer permitted to marry freely.

Common Misconceptions:

  1. Genetic genealogy  is just for fun.

There is no doubt that genetic genealogy is a fun and interesting new way to  explain genealogy. “Finding Your Roots” and “Who Do You Think You Are?” uses DNA testing to support and augment the powerful stories shared by celebrity guests; leading many thousands of people to purchase DNA tests to explore their roots. Awareness: Every testing company from 23andMe <www. 23andme.com>, AmcestryDNA <www.dnaancestry.com> and Family Tree DNA (FTDNA) <www.FTDNA.com> have very small databases of African-Americans and almost  non-existing databases of Africans. So you get something but perhaps not what you wanted. However, it is still a valuable tool in your genealogical arsenal. I have traced my ancestors back to 1460 Herefordshire, England. With DNA testing and other relatives testing I have been able to discovery new relatives unknown before. Results of four living relatives DNA results indicated a relations at 22-26 cm’s and a direct relationship to William Johns who was married to Ann Merryman. With this information I was able to discover African-American’s not recorded any place by Johns family genealogist.

2. Can women take a genetic genealogy test?

Women can take three of the four major genetic tests, and both males and females can benefit from the test results. The mitochondrial-DNA (mtDNA), autosomal-DNA test (atDNA), X-DNA. Y-DNA you will find that most companies will tell you it is for males only. True but you still can participate by finding a male member of your immediate family willing to get tested. Problem solved.

3. DNA will provide me with a family tree

What! DNA testing in no way can result in a family tree. There is no magic bullet for revealing your family tree. In conjunction with sound genealogy research and genetic genealogy it can help you build your family tree. No work no tree.

Facts, all DNA tests are not equal, all testing companies test at different markers and some companies or websites do no testing at all but send your sample to a company like 23andme. They also may not keep your raw data so you are out of luck if you can not retrieve your data. Some say they will provide a ethnicity report and if they are taking about 37 markers good luck (Y-DNA). All testing companies use laboratories across the country and that you need to review. Some companies provide what I call shop talk with very little value to you but ask any way, what logarithm do they apply to your data?

Marker – a gene or a DNA sequence which has a known location on a chromosome. This includes a single nucleotide polymorphism (SNP), short tandem repeats (STR) and any location in the DNA that is associated with a trait or a disease. In genetic genealogy, the results of testing various markers help determine how recently a common ancestor may have lived. Y-DNA (Y-STR) test can be purchased in sections from some companies. Family Tree offers Y-DNA12, Y-DNA25, Y-DNA 37, Y-DNA67 and Y-DNBA 111 STR marker tests and also SNP testing. AncestryDNA offers a Y-Chromosome test for either 33 or 46 marker locations, but does not provide SNP testing. The National Geographic Geno 2.0 test is an extensive array of Y-DNA SNP’s and is expensive.

Centimorgan (cM) – a centimorgan is a measurement of how likely a segment of DNA is to recombine from one generation to the next. Places on the chromosome that are one centimorgan apart have 1 percent probability of recombining during meiosis. The higher number of centimorgans, the closer the relationship.

Sources:

http://www.23andme.com

http://www.dnaancestry.com

http://www/ftdna.com

http://www.isogg.com

http://www.monacannation.com

http://gliesians.com/

https://www.genome.gov/

https://genographic.nationalgeographic.com/

 

 

 

 

 

 

Discover Your Roots with an African DNA Test, Why Test and What test does what for you?

Discover Your Roots

 

After many hours and days exploring the literature on DNA testing and the pros and cons to testing, not to test, what to test for, what companies are best to meet your needs, all the testing possibilities, procedures, logarithms used by each company, results in simple terms you can understand, were to place your raw data after the test and what companies will secure your information it seemed appropriate to blog this to you.

Many African-Americans and others are using an African DNA test to get answers about their ethnic ancestry.

Typical questions include the following:

  • How much of my genetic heritage is African?
  • What regions of Africa do my ancestors come from?
  • Where does the remainder of my heritage come from?
  • Is my African ancestry from my father’s lineage or my mother’s?
  • Do my physical features reflect African ancestry or something else?

Fortunately, there are several reasonably priced African DNA tests that answer these and other questions about one’s ethnic ancestry.

The tests all use home test kits and sample collection is easy and painless. Depending on which company you use, you might wipe some cells from inside your cheek with a little swab or spit some saliva into a tube. No blood is required.

Here are my top seven recommendations for anyone interested in an African DNA test.

1. Ancestry DNA

AncestryDNA (http://www.ancestry.com) recently rose to the top of this list. Both men and women can take the test and it will identify other people in the database who share common ancestors with you. It is an autosomal test similar in technology to Family Finder (http://www.ftdna.com) and 23andMe (http://www.23andMe.com), discussed below.

The test includes an Ethnicity Estimate that summarizes the percentage contributions of different regions of the world to your overall ancestry. That estimate now breaks African Ancestry into nine regions:

  • Africa North
  • Senegal
  • Ivory Coast / Ghana
  • Benin / Togo
  • Cameroon / Congo
  • Mali
  • Nigeria
  • Africa Southeast Bantu
  • Africa South-Central Hunter-Gatherers

This is the first widely recognized, legitimate DNA test to provide this detailed a breakdown of African ancestry

2. Family Finder, which includes Population Finder

Family Finder is an autosomal DNA test from Family Tree DNA. It’s widely used by genealogists, including those interested in African American genealogy.

The company will compare your DNA against a database of other users to find genetic matches. Most often these genetic matches will be cousins, having a common ancestor with you somewhere in the last five or so generations.

By emailing your matches you can connect with previously unknown relatives and learn much more about your family tree.

As part of the Family Finder test, you receive a myOrigins report, formerly called Population Finder, where the company compares your DNA with over 60 reference populations from around the world. This is a biogeographical analysis of the DNA you received from ALL of your ancestors.

The African part of your DNA may place you in any of four sub continental groups based on similarities to certain scientifically studied populations. The groups and populations are as follows:

  • Central African: Biaka Pygmy, Mbuti Pygmy
  • East African: Bantu (Kenya)
  • Southern African: Bantu (South Africa), San
  • West African: Mandenka, Yoruba

Very few people outside Africa are 100% African. Population Finder will classify the remaining portion of your ancestry using other populations.

3. Y-DNA Test at Family Tree DNA

Family Tree DNA also offers a Y-DNA test, which tracks your paternal line. Since only men have a Y-chromosome, only men can take this test. But women can still test a man from their paternal line, e.g. a brother, a father, a brother of your father, or a son of your father’s brother.

Like Family Finder, this test finds genetic matches who share a common ancestor. But with the Y-DNA test you know the common ancestor has to be a male in the direct paternal line like your father’s father’s father etc.

The Y-DNA test will also predict a man’s Y-DNA haplogroup. And many haplogroups are clearly tied to origins in sub-Saharan Africa. This is the real indicator of your paternal line’s ethnic ancestry.

TIP: If you’re interested in finding genetic matches, you should order the Y-DNA 37 test, which checks 37 markers. But if you’re only interested in determining your haplogroup, you only need 12 markers. I suggest you go to Family Tree DNA and look for the combination package of Family Finder plus Y-DNA 12. The combo price is an excellent buy.

If you later decide that you want to discover your precise position in the Y-DNA tree of life, you can upgrade to more markers or even order a Deep Clade test. That will tell you exactly which subclade of your haplogroup you’re in. In many cases this can tighten the geographic origins of your paternal line.

4. mtDNA Test at Family Tree DNA

Both men and women have mitochondrial DNA (mtDNA) to test. But only women pass it on to their children. So mtDNA is the test to track your maternal line. That’s your mother’s mother’s mother etc.

As with the test described previously, you will probably see matches with other users. But mtDNA mutates so slowly that your common ancestors may have lived thousands of years ago. That makes mtDNA less useful than Y-DNA as a genealogy tool.

Still, mtDNA also has a haplogroup that relates directly to the origins of your maternal line. And some of those are clear indicators of African origin.

5. 23andMe Which Includes Ancestry Composition

23andMe is another autosomal DNA test like Family Finder. This test can also serve as an African DNA test, because it has an Ancestry Composition feature that tells you what parts of the world your ancestors lived a few hundred years ago.

This admixture report is similar to the Population Finder feature of the Family Finder test. It reports on African Ancestry from these three regions:

  • West African
  • East African
  • Central and South African

However, if you also test at least one of your parents on 23andMe, this test can split your ancestral percentages into your paternal and maternal sides.

23andMe also has a DNA Relatives feature that’s similar to Family Finder and it will estimate your Y-DNA and mtDNA haplogroups. So if you want to cover all your bases—then the 23andMe test can be a great value as an African DNA test.

6. Y-DNA and mtDNA Testing at African DNA

Harvard University Professor Henry Louis Gates, Jr. was a pioneer in African DNA testing. He founded African DNA to encourage more African-Americans to get their DNA tested.

The company offers a Y-DNA test of 25 markers and an mtDNA test like the mtDNA Plus test at Family Tree DNA. In fact, Family Tree DNA is affiliated with the company and does their DNA testing.

Now they can also offer the Family Finder test that they renamed Ancestry Finder.

Note that African DNA only offers one paternal line Y-DNA test and one maternal line mtDNA test. They do not offer additional Y-DNA markers, the Full Mitochondrial Sequence (FMS) test, or Deep Clade testing. You need to order those tests directly from Family Tree DNA.

The African DNA web site does have more content specific to African DNA testing than any of the more general DNA testing companies. So I encourage anyone looking for an African DNA test to visit the site and learn all you can.

Uniquely, African DNA does offer some higher priced packages that combine DNA testing with genealogy research to build your family tree.

For most African-Americans there are no genealogical records prior to the 1870 census, when last names of former slaves began to be recorded. If you want someone to build a few generations of your family tree, however, this is an option to consider.

MONEY-SAVING TIP: If you’re not ordering a package with genealogy research, be sure to recheck Family Tree DNA to compare prices before placing an order with African DNA. At the time of this writing, you can order the same Y-DNA and mtDNA tests directly through Family Tree DNA for significantly less money.

7. Y-DNA and mtDNA Testing at African Ancestry

African Ancestry is another company that specifically features African DNA tests. Like the companies above, they check your Y-DNA and mtDNA to determine your paternal and maternal lineages. Since their web site does not provide details of either test, I cannot compare them.

Unlike Family Tree DNA, they do not keep a database of customer results, so you will not receive any matches to people with similar DNA. Since the company does not have an autosomal test like Family Finder and 23andMe, it cannot provide any admixture percentages. You won’t learn anything about ancestors outside your narrow paternal and maternal lines.

I found some interesting data on the web site. Even though this site specifically attracts people of African descent, 35% of the paternal line tests show European ancestry. Much of that non-African DNA was introduced into the family tree during the era of slavery. In addition, 8% of their maternal line samples show non-African haplogroups.

An article in the Wall Street Journal was critical of the African DNA test reports provided by this company. Independent experts say that mitochondrial DNA is not sufficient to nail down an ancestor’s origin to a specific country.

Furthermore, the large migrations of Africans over the last 3,000 years means that the typical black American’s DNA will match Africans living today in several countries. Even the founder of African DNA was quoted in the article that the country-specific reports his company provides are largely a “best guess.”

The testing prices at African DNA are higher than those of the companies listed above. Even if you have your African DNA test done elsewhere, the African Ancestry web site includes some interesting information on African heritage and a list of country-by-country resources in Africa for genealogists.

Other African DNA Tests of Uncertain Quality

DNA Tribes uses autosomal markers representing all your ancestors. But unlike AncestryDNA, Family Finder and 23andMe, which check nearly a million autosomal SNPs, DNA Tribes checks a maximum of 27 STRs.

I won’t try to explain the difference between an STR and a SNP h//ere. But autosomal STRs are what police forces around the world have been collecting from criminals for decades.

The company examined 383,000 STR records and claims to have identified major genetic regions around the world. They compare your DNA with their proprietary database and issue reports on your most closely matched regions.

The company does not share its database or reveal its methods. And independent experts are skeptical when such detailed reports arise from so few markers.

Roots for Real offers Y-DNA, mtDNA, and an autosomal test based on 16 STR markers. They position their autosomal admixture test as an African DNA test. But their database is only about one third the size of the already questionable DNA Tribes test. And all of their tests are overpriced compared to market leaders Family Tree DNA, 23andMe, and Ancestry.com.

Warning: These tests are based on sound science. But if you don’t know exactly what you’re doing, you can take the wrong test for your situation. It’s also easy to pay too much…settle for incomplete data…or misinterpret the results.

My test:

Y-DNA 111 markers, mtDNA + Plus, Full Sequence DNA and Family Finder DNA

My Haplogroup: Y-DNA (E-M2) and mtDNA (L2a1a2

 

 

Sources:

http://www.23andme.com/DNA assess 2/10/2017

http://www.ancestry.com/DNA assess 2/10/2017

http://www.myheritage.com/DNA assess 2/12/2017

http://www.africanancestry.com/home/ assess 2/04/2017

https://www.africandna.com/ assess 2/04/2017

http://www.FTdna.com

Megan Smolenyak Smolenyak and Ann Turner, “Trace Your Roots with DNA” published 2004

Blaine Bettinger, “The Family Tree Guide to DNA Testing and Genetic Genealogy” published 2016

Haplogroup

 

The Legal Genealogist: Term of the day: haplogroup

 

Source: http://thelegalgenealogist.com dated 22 Feb. 2017

This article was written from a Eurasian perspective. The definitions are correct.
The genetic genealogy glossary defiunition of haplogroup is “a genetic population group of people who share a common ancestor on the patrilineal or matrilineal line. Haplogroups are assigned letters of the alphabet, and refinements consist of additional number and letter combinations.”1

Okay. Great. What’s that mean?

Basically, if you think of all humans who’ve ever lived as part of the human race as a family tree, our haplogroup is what branch of the tree we can park ourselves on.

Everybody — male and female — has at least one haplogroup: our maternal haplogroup, as defined by our mitochondrial DNA (mtDNA). That’s the kind of DNA we all inherit from our mothers and that only females pass on to their children.2Our mtDNA haplogroup, then, is the branch of the tree we’re sitting on when the roots go back to the first woman from whom we descend: our mother’s mother’s mother’s mother.3

By itself, the mtDNA haplogroup tells us a great deal about our very deep ancestry many generations, even thousands of years in the past. But it also has some information we can use right now. It can tell us, for example, if our direct maternal line is of recent African or Native American origin. Or whether you, like me, have a maternal line that’s plain vanilla European.

Note that the fact that my maternal line is plain vanilla European doesn’t rule out having some more interesting ancestor from Africa or with Native American origin — it just means it isn’t my direct maternal line. It’s not in the direct line from my mother’s mother’s mother’s mother.

Only one of the major genetic genealogy companies offers mtDNA testing: Family Tree DNA. When you test at the HVR1 or HVR1+2 levels, the test looks at enough of the genetic markers to tell you what broad branch you belong to, represented by a letter like K or H. To get the specific branch — or twig! — the full mitochondrial sequence test (FMS) tests the entire mitochondria.4

Men also have another haplogroup, carried in their YDNA. That’s the kind of DNA that only males have and that’s passed from father to son largely unchanged through the generations.5 The YDNA haplogroup, then, is the branch of the tree a male is sitting on when the roots go back to the first man from whom he descends: his father’s father’s father’s father.6

By itself, the YDNA haplogroup tells the tale of deep ancestry just as the mtDNA haplogroup does, can indicate specific types of recent ethnicity — and is particularly useful genealogically to help distinguish between groups of men of the same surname: in my own research, for example, we thought our Shew line might be related to a specific Pennsylvania Shew line until we found that our line was haplogroup I and the Pennsylvania line was haplogroup R. Different branches of the human family tree entirely.

You will get a prediction of your YDNA haplogroup when you test with 23andMe and can get very specific YDNA haplogroup data from YDNA testing with Family Tree DNA, the only major genetic genealogy company that offers YDNA tests.


SOURCES

  1. ISOGG Wiki (http://www.isogg.org/wiki), “Haplogroup,” rev. 27 Dec 2016.
  2. Ibid., “Mitochondrial DNA tests,” rev. 15 Jan 2017.
  3. And so on back into time, often well before genealogical time. And see ibid., “Mitochondrial DNA haplogroup,” rev. 24 Sep 2017.
  4. Ibid., “Haplogroup,” rev. 27 Dec 2016.
  5. Ibid., “Y chromosome DNA tests,” rev. 4 Dec 2016.
  6. And so on back into time, often well before genealogical time. See also ibid., “Y-DNA Haplogroup ages”, rev. 19 Oct 2013.
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