Haplogroup L

[cacio]

Sw33tdecent:

half of your DNA comes from your father. However, which part of the DNA your father gives you is random. May be most of the DNA your father gives you comes from your paternal grandfather, but may be most of it comes from your paternal grandmother. Each chromosome (except the Y chromosome) is a mixture of all your previous lineages. Theoretically, you could have none of the DNA of your paternal g-g-g-grandfather, or you could have a lot of it.

The peculiarity of mtDNA and of the Y chromosome is that they are passed on as a whole without mixing. So the mtdna is exactly the same as your female ancestor hundreds of generations ago (plus of course the intervening mutations), and you can trace a lineage. In other words, you are 100% sure that the mtdna is exactly what you got through the female line, and the Y is exactly what one got down the generations through the male line. You cannot do that with the other chromosomes.

However, you can trace individual genes across generations. Indeed, that's what happens with most genetic medical tests. If there is a disease anywhere in the family (father/mother/etc.) one can test oneself and see whether one has the particular gene.

cacio

[Sw33tdecent]

But the autosomal test is use to determine paternity? If that is the case, then how could I (a female) use it to determine my father's haplogroup?

[jaynegen]

Autosomal DNA

The autosomal dna gives the alleles from both parents.

[Sw33tdecent]

Okay, I have a question, a silly one but it needs a response. Granted I understand that the mtDNA is used to test your mother's mother mother (etc) lineage. And is one of the few test offered to woman. But why is that have of our genetic makeup is comes from each parent. If that is so then why is familytreedna (or another DNA testing site) unable to test a woman for her father's lineage using DNA.

Now bear in mind that I understand that the y chromosome in males is what is being tested for the father's father fater (etc) lineage. I just can wrap my head around the fact that 1/2 of our genetic makeup is being ignored because the sex one was born into.

[cacio]

Sw33tdecent:

... but then it is not fair that women have two X chromosomes instead of one ...

cacio

[Sw33tdecent]

That would be so cool to do. Except there is only one major problem, I am a female. And since I am having my mtDNA done it does not make sense to test my brother for the same test (unless my theory of being adopted is true!!!). Curses to all the men, it is not fair all the test are mainly performed on you.

[lgmayka]

No the other site was genebase.com.

FTDNA does seem to offer a mild discount for yDNA transferees from other testing companies, but the offer seems not to apply to mtDNA:

http://www.familytreedna.com/PDF/PROMO_GAP.pdf

And besides, when FTDNA renewed this promotion on October 26, they did not say when the offer would expire.

[Sw33tdecent]

lgmayka,

No the other site was genebase.com. I asked if the samples could be transferred before I purchased the kit and was told no. The other site does have a genealogical and surname project as well. But I find the prices here on familytreedna to be more affordable.

[lgmayka]

By the way, the results below were obtained from another site, where I only had my HVR-1 sequenced. I am waiting to receive my kit from familytreedna.

Was the other site the Genographic Project? If so, you don't need a new kit. You can transfer your Genographic results directly into an FTDNA account, and then order more tests (on your existing samples) there.

To do this, click the "Learn More>" hyperlink at the bottom of your Genographic results page.

[vraatyah]

The last question currently on my mind, relates to the six mutations (whatever that means, cause I am not a mutant. Not that would be a bad thing, any way). The first three mutations have a strong relationship to L3f, M7a, and W. What does this mean?

a bunch of mutations should be treated as a whole, because a single mutation usually is not unique for the haplogroup this lineage falls into.

[Sw33tdecent]

Haplogroup L3f

Hi, I am recently new to familytreedna. I have a few questions, but I am not sure if this the right place to ask them. But I am willing to give it a try in hopes of getting more knowledgeable information.

First off, does anyone know what duplicate DNA is being used to test against all the DNA samples that are received? How is it determined that the substitution (in my case) is do the random repeats "thought" to exist in a particular ethnic background? How can it be determined that these substitutions, deletions,or insertions are not a result of poor genes, enviroment, random selection, etc....

The last question currently on my mind, relates to the six mutations (whatever that means, cause I am not a mutant. Not that would be a bad thing, any way). The first three mutations have a strong relationship to L3f, M7a, and W. What does this mean?

By the way, the results below were obtained from another site, where I only had my HVR-1 sequenced. I am waiting to receive my kit from familytreedna.

Thanks


Location........Region.......Mutation Type.......Nucleotide......Haplogroup
16209...........HVR-1.........Substitution.............T > c...........L3f
16218...........HVR-1.........Substitution.............C > t...........M7a
16223...........HVR-1.........Substitution.............C > t...........W
16292...........HVR-1.........Substitution.............C > t...........M7a1
16311...........HVR-1.........Substitution.............T > c..........M10
16519...........HVR-1.........Substitution.............T > c..........N

[GregKiroKHR1bL1]

Ibo and Bantu mtDNA Similar: The Ibos live in Iboland. It comes as no surprise that the stifling heat of central Africa would dictate the type of clothing worn by any native peoples. The Ibos wear little or nothing until they reach puberty. At this time, the men usually wear loose-fitting cotton shirts and a loincloth, while the women wrap different pieces of cloth around themselves and also wrap some cloth around their head. The men often carry machetes, useful for clearing overgrown paths and offering protection for wild animals. The Ibos are profoundly religious. These polytheistic people worship many gods. They believe that there are three levels of divine beings: the highest level is the supreme god, or “Chukwu.” Underneath Chukwu are lesser gods, called “Umuagbara”, and under these are the “Ndi Ichie,” the spirits of dead people. The Ibos also believe in reincarnation. They see death as a transient phase between life and the spirit world. When someone dies, he or she starts a new life in the spirit world. After a time in the spirit world, a dead person would be reborn as a new person and the cycle would continue on. Each village has priests and priestesses who help in all spiritual matters, conducting ceremonies and rituals. And since the Ibos believe that everything in life is controlled by higher powers, there are also diviners in a village that attempt to predict the future. The language of the Ibos is very interesting. It is derived from a group of languages commonly found in West Africa, the Kwa languages. It is based a lot on pitch, vocal inflections, and context when defining the meaning of a word. A single word can have numerous meanings depending on these factors. Idioms and proverbs play an important role in the Ibo language. Someone who does not use them in speech is considered a novice at speaking the language. http://www.mnsu.edu/emuseum/cultural...boculture.html

The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n = 32), J (n = 4), K (n = 5), T (n = 2), U5 (n = 6), U6 (n = 9 also known from North Africa), A (n = 12), B (n = 7), C (n = 4), and M (n = 16), respectively. The European Caucasian and East Asian haplogroups are expected due to admixture between individuals with recent ancestry in Western Eurasia and sub-Saharan Africa.

Forensic Science International

Volume 148, Issues 2-3 , 10 March 2005, Pages 169-179

I did not find any close matches to my HVR-1 markers. There were some matches to only my HVR-2 markers. However, no matches to my HVR-1 & HVR-2 markers. The haplogroup is assigned by a motif. My HVR-1 & HVR-2 match two motifs. Also, T16086C ( http://www.isogg.org/ for HVR-1 AF254446) is a Neanderthal marker as is C16223T. Only a few matches will go back very far in time. Recent matches will be exact (or almost exact).

L1c1b and L1c1c

L1c (root type)

16129–16187–16189–16223–16278–16294–16311–16360 (073–151–152–182–186A–189C–195–247–263–297–316)

L1c1b — add 16293 ( lose 195–297)

L1c1c --- add 198 and add 16293

Bantu and African Americans account for most of the variability of the rest of the network; they represent 84% of the sequences belonging to L1c1b and 95% of L1c2. . . . African-Americans account for 69% of L1c1c sequences. . . . The remaining L1c clades—L1c1b, L1c1c and L1c2 . . . are mostly composed of Bantu and African American individuals (98%), whereas Pygmy presence is limited to two haplotypes (three individuals). Bantu populations are thought to have spread into this [Central Africa] area only 2–3 kya, in the course of their expansion through sub-Saharan Africa (Cavalli-Sforza, 1986).

Batini, C. et al., Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa, Mol. Phylogenet. Evol. (2006), doi:10.1016/j.ympev.2006.09.014

[cacio]

kokeb:

presumably the Pygmy matches on your Ancestral Origin page come from some of the papers you mention, perhaps the Salas one. Obviously, native Africans or Pygmies aren't really purchasing NG kits...
Perhaps the actual sequences of these groups are available through the authors, though I don't have them.

Once an author identifies a subhaplogroup, the classification is effective (unless it is later proved inaccurate). It's just that it takes time for people to absorb the new scientific papers. FTDNA especially is a few years behind. They constantly update things like European H (for which there are thousands of potentially paying customers), but for things that are much rarer (like L1c) they don't bother too much.

cacio

PS: by the way, although I am European (Italian), I actually have no matches, nor anything in my ancestral origin page. As soon as you leave the standard European haplogroups, this is the most common situation. The same goes for my Y chromosome.

[kokeb]

Wow cacio. My head is still swimming from all the articles you sent me. Overnight I went from knowing next to nothing about my haplogroup to knowing a lot.

I have no HVR1&2 matches but here is what my 'Ancestral Origins' page states for HVR1 matches:

L1c Africa (712) 1
L1c* Central African Republic (14) Biaka 4
L1c* Central African Republic. (21) W. Mbenzele Pygmies 3
L1c* Spain (546) 1

As you predicted most of the matches are related to the Pygmies in the Central African region. This also is in agreement with the paper you sent me "Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa". Like you stated, based on my HVR1&2 it does look like I would fall into what they classify as L1c4 . Though it looks like the paper was trying to propose these classifications and I'm unsure if or when they will be put into effect.

I hope that they send researchers out to this area again to collect more samples; in the paper they state that they are the first to collect from the Babinga people which makes me wonder how many other African populations are still missing from this database. I wish we could see a country by country breakdown of all the populations sampled... And where more population sampling is currently taking place... It's always good to know the current states of things and to see progress, that's my opinion anyway.

Thanks again for all the information you sent me Cacio; I'm finally starting to understand so much. I'm even reading through the other forums with a new level of understanding where before I'd have just stared and thought "huh???". Now if I could only find some matches...

[cacio]

kokeb:

L1c is a deep and ancient lineage (dating perhaps 90K years ago), present mostly in Central Africa (Cameroon,Congo, Angola), and less so in Western Africa. It is very frequent among the Pygmies, especially some particular subgroups (like L1c4 and L1c5).

cacio