Wednesday, March 2, 2016

That Y-chromosome (part 3)

Since our Y-chromosome found its way out of Africa, a number of pathways were followed.  The Mediterranean Sea placed a coast line which provided a road to split that Y-chromosome east to west.  The northwestern coastal group soon ran into other geographic boundary's with the Black Sea being northwest, and Caspian Sea being northeast, and the Caucasus Mountains in between.  It was around this 550 mile mountainous system that our R-haplogroup is thought to have first appeared.  I suspect that the ice curtain that kept going up and down also had something to do with the next migration groups.  The R1-haplogroup scattered about leaving this Y-chromosome as far northeast as the slopes of the S. Ural mountains [Bashkirs]  and the Basque area of western Europe.

Central Europe seemed to be one place that the R1b - haplogroup settled around those salt mines that were so important for early human survival.    For our JONES surname things [genetically] took roots both in culture and language.  Expanding their horizons they moved about the Iberian peninsula [and other places] and finally found their way up St. George's channel to place their Y-chromosome among the islands.  For R1b1a - haplogroup [roughly 75% of us with the JONES surname ] the Welsh (Anglesey) at 89%, and Basque area (French, Spanish) at 88%, and the Turkic people (Bashkirs) were found with 86%. [confines of S.Ural mountains]

For those interested: 1) Irish = 82% , 2) Scots = 77%, 3) Spanish (Minorca) = 73% , 4) Dutch (Germanic west) = 70%.  What a deal...that same Y-chromosome is found among most of those with the JONES surname of Welsh descent.

Monday, February 15, 2016

That Y-Chromosome (part 2)

The runt of the litter it is as shown by the last post.  Its linear array of genetic information carries 78 genes.  Now if you can imagine pushing this little fellow from the top down, forcing it flat on a page of paper, you might get something like this:

The 78 genes line up along a physical structure [called a helix ] with the genetic code written along in units of three molecules [each molecule called a nucleotide] to make directions for its protein.  Now on the Y-chromosome when one of these nucleotides get replaced by mutation, this becomes an identifiable marker.  It is a "single"..."nucleotide"..."polymorphism" [change] which is labeled "SNP".

The markers that have become recognized as distinct changes to tag for various genetic groups have been discovered.  For the haplogroup R they are shown above.  Each marker has a specific physical location along the genome.  When this marker is found by DNA testing, it can identify a ethic group which has past on these changes.  For haplogroup R, this change is believed to have occurred some 30,000 years ago, and has been labeled M173.  The R1b marker is labeled M343, and the R1b1a2 marker is M269.  It is interesting that the M269 marker is believed to have occurred some 5,000 to 8,000 years ago which is also the time that the English Channel was formed.  At any rate, the following chart shows a big picture of the hapogroups as they have been thought to happen along the sands of time.

You can follow each haplogroup and its believed date of mutation.  This is for the Y-chromosome only...what a deal for this little runt.

Note: The drawing above does not show the exact physical location along the genome of each mutation.  It is drawn as an example.  The "Gene Tree Haplgroups" I created for my own understanding some years in the past.  Hopefully it will provide another way to visualize the chronology of this Y-chromosome.

Sunday, January 17, 2016

That Y-Chromosome (part 1)

All this recent DNA stuff has gotten beyond confusing.  Haplogroups, haplotypes, DYS#, locus, alleles, marker numbers, clades, subclades, mtDNA, autosomal DNA, SNPs, STPs, MVPs, MTVPs, big-Y or something like that; and on, and on, it goes.  Not too long ago, it was just the Y-chromosome, a 12-marker test, a snip or two, and off you went to that DNA sunset.

Not any more it seems.  What's one to do?  A "big" picture came to mind...that "Y-chromosome" started things off. [actually it was that mtDNA = Seven Faces of Eve... but for me things got started climbing my own family tree through the male descent].  At any rate, a "big picture" removed from all that word soup might be of help.  So here goes.

The Y-chromosome carries the linear array of genetic information essential for male sex determination.  It is the smallest of all the chromosomes.  To give you a visual picture of its related size to the other chromosomes, I have traced an image from the late prophase (a stage during its duplication phase) of a normal male karyotype. (a way the chromosomes can be visualized by their size, shape, and number)

Here you have it...the runt of the litter.  Chromosome #1 [the largest chromosome in size] is shown in comparison to the Y/X chromosome which would be numbered #23.  It only carries 78 genes, whereas the X-chromosome gene carries around 2,000 genes.  Doesn't seem fair...does it..., but its advantage is that it contains the largest "nonrecombining block" in the human genome. [nonrecombing portion of the Y-chromosome written = NRY]  In 1997, a way to detect changes [mutations] was formalized called "denaturing high-performance liquid chromatography", so off to the races it was.  The "Y Chromosomes Consortium Cell Line Repository".  The study of mutations [called polymorphisms] on the nonrecombining potion of the Y-chromosome.  Who would have guessed from the runt of the litter.

The tracing shown above is made from "figure 7-6. Karyotype of normal male, with chromosomes in late prophase" p. 278 , Nelson Textbook of Pediatrics, Behrman(Ed.), 4th Edition, Saunders....a text from my medical practice.

Tuesday, December 15, 2015

R1b1 Distribution

Thought it would be helpful to outline the distribution of the R1b haplogroup.  My own JONES surname haplogroup is R1b1a2.  The counties (areas) with the highest per cent are listed:

Welsh (Anglesey)                            89%  n=88
Basque (French/Spanish)                88%  n=67
Bashkirs (Turkic People)                86%  n=43
Irish                                                 82%  n=222
Scots                                               77%  n=61
Spanish (Minorca)                          73%  n=37
Dutch (Germanic West)                  70%  n=27

For those of Welsh we are...right at top!  That Celtic genome it is.

Saturday, October 24, 2015

Discussing DNA - As A Genealogist

At the cellular level, the human species functions under the directions of DNA.(1)  For each individual, this DNA is a unique combination of certain molecules passed down; half from father, and half from mother.  This combination is held within a specialized structure called a chromosome.(2) There are 23 pairs of these DNA carrying structures, resulting in 46 total individual chromosomes.  [22 pairs are called autosomes(3), and 1 pair is called germ cells, or sex chromosomes.  Some get all the fun!]  All lumped together, this is called the genetic material from which we all exist.

     The purpose of these chromosomes are to deliver a correct copy of itself to each daughter cell. When these copies are changed from their original form, they are called mutations.(4)  These mutations are permanent alterations that can be passed down the family tree, one generation to the next.  These changes can occur at a single site (point mutation), or involving the insertion or deletion of a number of genetic sites. (variable or multiple site mutation)  These changes, when recognized, have become "markers" among certain genetic groups that become a method of ethic identification. [haplogroups to haplotypes]

For the genealogist, the most important markers occur on 1) the Y-chromosome. [one of the sex chromosomes], 2) specialized DNA found in the ribosomes(5) of the mother in structures called mitochondria (6), and 3) on any other of those chromosomes called autosomes.

A series of drawings are shown which represent these concepts:

Y-chromosome DNA which is passed down from father to son on the "Y"  sex chromosome -

Squares and circles are drawn to represent the male [square], and female [circle].  The mutation found on this chromosome is a single [point mutation] called SNP - pronounced "snip".

Mitochrondrinal DNA is inherited through the maternal line.

This collection of DNA is relatively small but necessary for the energy production in all cells. [For those interested this is called oxidative phosphorylation.  Leave it up to all the moms of the world!]
The term is given as "mt-DNA" where "mt" stands for mitochrondrial.

Autosomal DNA are markers identified among the chromosomes that are not sex chromosomes.  They are passed down from the ancestors as a group of markers.  They are used to make generalized ethic determinations found among the families' prior generations.  This is generally expressed as a per cent of each marker that occurs among the family group.  It does not show a direct descent from their parents to their children, only distinct mutations that have occurred among family members of past generations.

 Whew...what a deal!

* * * * * *

(1) DNA = deoxyribonucleic acid [pronounced = dee-ox-e/ rye-bow/new-clee-ick ass-id] At least from my Kentucky twang!

(2) chromosome [pronounced = chrome-o-zone]

(3) autosomes = any chromosome other than a sex chromosome [pronounced = auto-zone (s) ]

(4) mutations = the process where changes occur in the number or structure of the genetic material

(5) ribosome = a structure outside the normal location of regular DNA (in the cytoplasm) that is responsible for protein synthesis.  This specialized DNA is found in the structure called the mitochrondria

(6) mitochrondria [pronounced = mito-condre-ah] = semi-autonomous organelle (in all cells) which produces the energy for life called oxidative phosphorylation [pronounced = oxy-date-ive  phos-for-a-la-tion]

Wednesday, February 4, 2015

Haplogroup Geography

The various haplogroups have a distinct geographic distribution.  The following figure shows this distribution in broad general terms as the "per cent" of the haplogroups for certain parts of the globe.

The highest per cent for the geographic area outlined at the top of the figure, is shown in blue marker.  For example, haplogroup E is found in approximately 61% of those tested from "Sub-Saharan" Africa.  This same haplogroup if found in 53% of those tested from "North Africa".  Haplogroup J is found in 44% of those tested from the "Middle East".  My "JONES" haplogroup R is found in 45% from "Europe", followed by 41% from "South Asia", and 31% from "Central Asia".  For Wales it is found in 84%!  Move over Wales, here comes the JONES surname. [Interestingly haplogroup Q is found in 95% of those coming to the American continent.]

The data is taken from my research notebook 225B (RN #225B) titled "Human DNA - Out of Africa".

Wednesday, January 14, 2015

Haplogroups to Haplotypes

Our human genome has been around a long time.  Since its beginning, any random, permanent change in the DNA molecule has been called a "mutation".  A change in one nucleotide base pair represents a "point mutation", and is referred to in genetic lingo as "single nucleotide polymorphism" or "SNP" which is pronounced "snip".  The Y-chromosome is the smallest of those DNA chains called chromosomes, and is least likely to undergo mutations among all 46. [ that male stubbornness I guess]  Once a single base pair mutates, it becomes a distinct marker for that chromosome.  This marker is then past along among the male descendants.  These markers have been identified, and have come to be called "haplogroups".   They have been labeled using the alphabet A thru T, with "haplogroup A" starting things off.   The following chart shows these haplogroups starting around 60,000 BC.

As time has progressed, these haplogroups have undergone additional genetic changes, at various additional sites, involving multiple nucleotide bases. [Whew...can you keep that straight]  These are again random chances but involve at least two base combinations next to one another (tandem) or at different (variable) sites along the DNA molecule.  These additional changes among the "haplogroups" are called "haplotypes".  The number of haplotypes vary, and those haplogroups with the highest number of haplotypes are shown in the figure above.

Haplogroup "E" has the highest number of haplotypes with 58.   This is followed by haplogroup "J" with 34, and haplogroup "O" with 31.  My JONES surname haplogroup "R" comes in forth with 29 haplotypes.

Now if you take the number of haplogroups and divide by the number of "1000 year of existence", you come up with a ratio of mutations per thousand years!   For example, if you take haplogroup "E" with its 58 haplotypes and divide by 50 [ the number 50,000/1000 = 50] you get a ratio of 1.16 mutations per 1000 years.  If you take my JONES haplogroup "R" [29 divided by 30,000/1000 ] you get a ratio of .967 per 1000 years.  However, if you take haplogroup "J" [ 34 divided by 25,000/1000] you get a ration of 1.36 mutations per 1000 years.  How about get roughly 1 mutation per 1000 years for the haplogroups.  Haplogroups to haplotypes...part of our human family tree.

Data taken from "Y-Chromosome Phylogenetic Tree" from Genome Research and Family Tree DNA.