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 descent...here 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 that...you 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.


Saturday, March 29, 2014

A New Blog

Can you believe it...a new blog on "Networking Jones Genealogy".  One theme is of course DNA and those with the JONES surname.   It's goal is help provide a location for those who share an interest in this topic (subject) along with a number of other subjects that are important in this tree climbing thing called genealogy.  You can check this blog at:

     http://tjgnjg.blogspot.com for a statement of goals and the purpose of the blog.

If you have an interest in any of the themes, please let your self join in the networking with others who share this terminal illness.  Networking Jones Genealogy is the name.

Monday, June 17, 2013

12 Marker - Exact Matches

The folks who have shown a 12 marker exact match to my own DNA have some very different sounding surnames.  Say what!...was my first response to this finding.  These folks were to have shared a common ancestor some 1000 years ago. [Roughly around the time of the Norman invasion to the island.]  The following are those surnames.

Amshoff
Boyle
Claxton
Doharich
Sharp
Gilmore
Johnson
Weirich
Pritchard
Gill
Leonard
Pearson
Fouriner
Uttridge
Muradoglu
Maudire-Janton
Tilton

... say what!

Are there any folks out there with the surnames above who have done their DNA?  Would love to try and make the historical connections to these surnames?  Our common ancestors must have been close by around 1100 AD...!