Thursday, December 30, 2010

The Gene Tree, Haplogroups

Haplogroups are defined by their single nucleotide substitution called a SNP (snip). [single nucleotide polymorphism] Those in the know [researchers who have established the system of naming [nomenclature] have assigned an English alphabetical system starting with the letter A. This haplogroup is felt to be the oldest genome surviving since our earliest days. The figure to the right is my attempt at showing a "big picture" of this classification system. The dates generally believed to be starting points for each branch of this gene tree are given along the top ridge for each haplogroup. More than 60,000 years ago the human race is believed to have shared a common genetic message. At around 50,000 years ago the human genome started to branch, giving rise to several new DNA messages. Down through the ages, each branch developed a new haplogroup, passing its single nucleotide polymorphism down to the next generations. As time passed, these branches became the roots of our ethnic and cultural family groups. My JONES DNA is haplogroup R1b, believed to have branched from haplogroup R1 some 25,000 years ago. It was around this time that the earliest human burial has been described on the island that was to become my family's home. [The "Red Lady of Paviland" on the Gower Peninsula.] What a deal!

Wednesday, December 22, 2010

Terms, Terms, and more Terms

By now the poor brain should be spinning around the terms that are used to communicate information about DNA. This is especially true when ordering a DNA test, and the results are given in a bunch of different terms. Having some idea how all these terms fit together is a helpful thing. My own DNA testing results state:

"We provide the actual scientific Allele values and DYS #'s for your results unless the markers were discovered at the University...."

My results were given as "Panel 1 (1-12)", "Panel 2 (13-25)", and "Panel 3 (26-37). Under each panel the results were given as "Locus", "DYS#", and "Alleles". Wow! Terms, terms, and more terms...what is one to do?

To begin, a "Panel" is how the DNA testing is organized and actually carried out in a testing laboratory. Panel 1 is the first group of 12 genetic markers that have been accepted as the standard among all testing labs. The "Locus" is the assigned panel number that each marker has received beginning with number 1 to number 12 for Panel 1.[number 13-25 for Panel 2, and number 26-37 for panel 3] Each "Locus" number corresponds to a DYS# and Allele value. The DYS# and Allele values had already been described in separate research labs which would of course cause a great deal more confusion if each lab reported their results under different labels!

Now the term DYS# is an abbreviation for D = DNA, Y = Y-Chromosome, and S = (unique) Segment.
A unique segment is the part of the DNA molecule [in this case the Y-chromosome] that has undergone changes (mutation) among several nucleotides in a row. Remember that a change at only one nucleotide is called a SNPs (single nucleotide polymorphism). Changes that have occurred at more than one site in a row (segment) have been termed a "Short Tandem Repeat" or STR. These short, tandem (next to one another) repeats are identified along the DNA molecule at the address called "Allele Value". [The allele was the earliest concept of genetic addresses for the codons that produced a protein.]

Here is the key issue and perhaps the most confusing. A single nucleotide change (SNP) is a very rare occurrence. This change (SNP) is past down generation to generation among a family, thus an ethic group. The SNP is used to characterize a "Haplogroup". The STR (Short Tandem Repeat) happens all along the DNA molecule, and when analyzed together produce the genetic finger print that is called the "Haplotype". Haplogroup (SNP) - Haplotype (STR). Using the Y-chromosome, the haplotype should be the same or very close to all males in the family. It is the STRs that are used to match our ancestors. More to come.

Wednesday, December 15, 2010

Baby Blue Eyes

Eye color is one of those things that everyone recognizes. What color is his/her eyes? Blue eyes, green eyes, hazel eyes, brown eyes, and perhaps some shades in between are the basic colors. Your eye color is given to you by your parents. Mom and Dad transmit half of the information needed to make this determination. Once these halves are joined together in your DNA, they will determine which color comes shinning through.

As you now know, this determination is made by the message you carry on your DNA. A series of codons, which make up the "gene" for eye color, is strung along one of those chromosomes (DNA molecule). It has two sides...the one from Mom, and the one from Dad. Remember your dinning rooms? The one you stood in to image 3-D space is one side of this gene. Your bucket truck reaches out to the other side. If you are standing in your mother's dinning room, your father's dinning room would be on the other side. [the gene is the whole series of dinning rooms on both sides, stacked upon one another, running in opposite directions]

If Dad has blue eyes, and mom has brown eyes, brown eyes will win out every time if Mon only carries the brown eye message on both sides of her DNA. [Brown eyes are called dominate.] If Mom carries a brown eye/blue eye gene, then it is possible to transmit blue eyes to a child. [one blue side from Dad, one blue eye from Mom] The blue eye color has been called recessive. Each side of this genetic message is now called an "allele". This term is important to know as we continue in our understanding of using DNA for genealogy. The "allele value" is the number giving to one half of the genetic marker along the codon (genome). It is like spray painting your side of dinning rooms, and spray painting the other side a different color. Thus each side of the gene can be classified by an address (allele number). The side for "brown eyes" and "blue eyes" will be labeled by a number. When you order a DNA test today, you will be given a series of "allele values" as results. These are the places along your genes that have been tested. The results of a 12 marker test is given by a series of numbers which identify the "alleles" that were examined by the laboratory doing the test. Baby blue eyes any one?

Friday, December 10, 2010

Mapping and Markers

Mapping the human genome was a daunting task. Starting in the early 1980s, The Human Genome Project began depositing enormous amounts of known DNA sequence information in very large computer databases. Over the next 20 years, the "big picture" became clearer. Most, if not all, of the human genome was successfully map around 2002. Since that time, this mapping has been used to help explore the "genetic" history of our human race. It became clear that the genes are DNA segments that encode information about an individual's heritable traits. Mutations are the original source of variation among these heritable traits. It ended up that most of these "mutations" (changes) are substitutions of one base pair (a single nucleotide, remember standing in your dinning room), for another. Once a mutation (SNP)is established, it is past down from one generation to the next. It has been estimated that about 10 million of these SNPs have occured in our human population. [see National Center For Biotechnology Information (NCBI)] Each SNPs is thought to have arose during the passage of time since our human history began.

Basic concepts have been developed that believe the greatest genetic diiversity of the human species is found in the the geographic area which it orginated. [known as Valilov's Concept] A mutation (change) found in the Y-DNA/mtDNA of a large number of people in various parts of the world most likely happened in a common ancestor. These changes can be "marked" and followed as "genetic markers". These genetic markers can be used to place that population group into a "haplogroup". More to come.

Tuesday, December 7, 2010

Easy way to Remember

You now know that the smallest unit of our genetic information is the triplet of nucleotides called a codon. To help our understanding, these have been represented using the first letter of each nucleotide's spelling. A is for Adenine, C is for Cytosine, G is for Guanine, and T is for Thymine. I seem to always have trouble remembering which nucleotide goes with what partner. To help me remember I use their alphabetical order A, C, G, T...then I remember that the ends meet. Thus A goes with T which leaves C to go with G. Easy way to remember.