Monday, March 13, 2017

Foundational Concepts of DNA

The DNA revolution has produced a number of new opportunities for the eager genealogist.  Along with these opportunities come a host of unusual terms, fancy words, and confusing outcomes that can make for some, a very difficult experience.  For those, who like me, continually express...say what!...this post will begin perhaps a series of posts on some basic ideas surrounding all this DNA stuff.   So, let's begin.

Our human existence is dependent on the cell, the basic unit of life.  All  "us humans" are made up of these cells, and come from cells.  As we know it, one of the most important aspect of these cells is reproduction.  [Good thing or we would'nt be here!]  At any rate, it is during this reproduction that our genetic traits get pass down.  Now this DNA ( doxyribonucleic acid ) is the molecule of inheritance for all.  These poor cell's DNA is the thing that gets knocked around in all these labs...scraped, dipped, broken apart, multiplied, electrified, analyzed, and...the results printed out, as the "Holy Grail" of our long lost relatives still among the family tree.

The basis for most traits past down is the functional unit of inheritance call the "gene".  Each gene is given a specific position (location or loci) along the DNA molecule to be preserved and transmitted on down the family tree.  These genes control our biological processes through the production of proteins and a special modification called RNA ( ribonucleic acid ).  The genetic composition of all genes is called the "genotype".  The observable inherited traits [ physical, behavioral, physiological, etc.] is given the word "phenotype".

Foundational concepts 1) Genes form the basis of our inheritance.

Monday, August 15, 2016

Haplogroup Hangouts

Our human Y-chromosome has experienced a number of mutations since the dawn of man.  On the most part, these mutations have been identified and given a standard nomenclature.   Called "haplogroups" , they have been organized by number [DYS #] and alphabetized A - T.  Their chronology has been estimated, with "haplogroup A" starting things off some 60,000 years ago, or so.  Their geographic locations have been identified.  The following figure was drawn some six years ago when trying to put all this DNA stuff together.  I thought it might be of interest in the very broadest sense. 

The haplogroups are shown in a chronological sense top to bottom.  The DYS # associated with each haplogroup is listed.  The general "hangout" for each haplogroup(s) is written underneath each.  The green swipe represents Africa with migration "out of Africa" identified.  Various colors then mark in the broadest terms, the migration patterns thought most likely for each haplogroup.  The JONES surname haplogroup is approximaly 75% R1b, and is shown by the darker blue line.

Give it a go.  If you see any errors or need for more recent information please comment.  Here you have my take on the haplogroup hangouts.

Wednesday, July 13, 2016

That Y-chromosome (part 4) Other Surnames

The particular haplotype R1b1a2 is one of the most common to carry the surname JONES.  It is also defined as R-M269 which is the genetic marker that is tagged for this group.  The following chart shows additional surnames that have been found to have the same marker [R-M269] from those who have tested their Y-DNA.  The listed is given in alphabetical order for the 61 other surnames that are found to match those with the surname JONES among my own DNA study groups.  What a deal!

When testing your own Y-DNA for your JONES surname, you may find that those among this list are more likely to match you than another JONES!

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.