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Snippets and References
see also Background Reading 
Personalities of the Past

1 DNA Glossary
2 Definitions 

3 Y Chromosome Traits
4 Atlantic Modal Haplotype
 
SNiPs & Haplogroups
R1b Haplogroup
                                                                   Migration to NZ From Wilts to Canterbury Plains 
5 An Interesting Case                            "Steadfast" its voyage and passenger list inc. Vines
6 Samuel Pepys Diary
                                                                   Bremhill Webpage
7 Mammals Chromosomes                This includes history, news, maps, a site under construction
8 Mutations                                               
Markers
Match Probability
Typical Mutations 

9 Dominant/Recessive Genes

10 USEFUL REFERENCES

In old English or Imperial measure 
1 hundred or hundred weight (cwt) =112lbs, 20 cwt =1 ton
1 quarter = 28lbs, 1 stone = 14 lbs
1 bushell (used for grain measurement) is a unit of volume or capacity in the British Imperial System, used in dry and liquid measure and equal to 2,219.36 cubic inches or 36.37 liters. Approximately a 13 inch cube.
1 mile is 1609 meters, 1 km is 5/8 of a mile

Money Value Conversion
Value of Goods & Services 1625
 
 
 
 

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1  DNA Glossary 
 ***allele 
variant of a gene or genetic marker. For STR markers, each allele is the number of repeats of the short base sequence. 
***base 
the building block of DNA, one of four molecules that link up to make a DNA chain. The four are named adenine, cytosine, guanine, and thymine (A, C, G, T for short). 
***buccal 
pertaining to the cheeks or the mouth cavity in general. Buccal cell samples for analysis can be obtained easily and painlessly
by a gentle brushing or scraping of the inside of the mouth. 
***chromosome 
one of the DNA macromolecules found in the cell nucleus. Humans have 46 chromosomes. See also X and Y. 
***DNA 
deoxyribonucleic acid. The chemical constituent of genes and chromosomes. DNA has four different base units, designated
A, C, G, and T, which are connected in long double chains, and the sequence of these bases encodes the genetic information. 
***DYS
DNA Y-chromosome Segment. A label for genetic markers on the Y chromosome. Each marker is designated by a number, 
according to international conventions. At present, virtually all the DYS designations are given to STR markers (a class often
used in genetic genealogy). 
***gene 
a meaningful sub-unit of DNA, encoding a protein. 
***haplotype 
a set of allele values of many markers measured for one individual and identified as coming just from one parent, particularly
markers on the Y chromosome. 
***locus 
(plural: loci) specific site on a DNA chain. 
***marker 
a distinctive sub-unit of DNA, generally not part of a gene. 
***STR 
Short Tandem Repeat. Also known as microsatellite. This is a genetic marker consisting of multiple copies of a short sequence
of DNA bases (typically three or four). Occasionally, one will mutate by the gain or loss of one repeat. 
***X 
one of the two sex-determining chromosomes, See also Y. 
***Y 
one of the two sex-determining chromosomes. A person with the combination XX is female, while a person with XY is male. The
Y chromosome, unlike the others, does not trade DNA with a "partner chromosome," and it therefore passes intact from father to
son. This property leads to a minimum of ambiguity in interpreting the results of Y DNA analysis. 

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2  Definitions
DNA: An abbreviation for deoxyribose nucleic acid, four varieties of which make up the complete molecular code for our genes. 
Most of us are more than 99 percent identical in our DNA make-up. It is the fraction of a percent variation among us that along
with environmental differences, makes us differ from one another. 
Genes: molecules comprised of thousands of nucleic acids. Our genomes are estimated to contain 40,000 to 70,000 genes.
Polymorphisms, literally meaning "many forms," are the often seen variations in DNA structure that are not usually associated 
with genetic disease. These relatively neutral small variants, because they are scattered throughout the genome, can be used to
locate genes to specific chromosomes and furthermore position those genes quite precisely on the chromosome. 
Genomes are the complete complement of our molecularly organized genes as well as a large fraction of other DNA whose 
function is not clear. 
Chromosomes are the paired tiny bodies of long segments of DNA contained within the nucleus of each cell. In humans there are
23 pairs of chromosomes. Each of us inherits one of each pair from one parent and one of each pair from the other parent. 
Nucleus of the cell. Inside each cell of our body, except the red blood cells, is a roughly spherical nucleus that contains all 23 
pairs of chromosomes. 
Cells are the tiny living compartments in all our tissues, the fundamental building blocks of our bodies. There are billions of them. 
X-linked recessive condition is a trait that is located on the X chromosome one of the sex chromosomal pair. A female has two X chromosomes. If there were a recessive mutation on one of them, the normal dominant variant on the other would cover up the 
condition and usually make its manifestation much less severe or absent. But the male has an X and a Y, the Y a tiny 
chromosome lacking the vast majority of genes on its paired X chromosome. So when an X chromosome with a recessive variant
on it is paired in the male with the Y chromosome, the mutated variant is exposed without a covering normal gene, and the 
disease is expressed. That is why X-linked conditions are predominantly seen in males rather than females. 
 
 

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3  Physical Traits Genetics on the Y Chromosome
Testing  of the Y DNA for genealogical purposes does not reveal physical traits, genetic diseases, health problems or longevity.
 Quote from Ms Ann Turner in  GENEALOGY-DNA-L@rootsweb.com mailing list of 5th March 2003: 
For the Y chromosome, there are very few genes, and the majority of those are 
concerned with sperm production. There is only one Y-linked trait which has 
been described by "classical genetics" (observations of how traits are 
inherited), and that is controversial. It's called "hairy ears," 
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?tool=bookshelf&call=bv.View..ShowSection&searchterm=y&rid=iga.section.d1e5150#d1e601
 
 

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4  Atlantic Modal Haplotype (AMH):
The descriptive term used by James F. Wilson to characterize the most common haplotype in parts of Europe. The markers and
repeat values For the AMH are; 
DYS19   =14 
DYS388 =12 
DYS390 =24 
DYS391 =11 
DYS392 =13 
DYS393 =13 
 
 

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5  An Interesting Case
http://www.hattiesburgamerican.com/news/stories/20030223/localnews/1042775.html 
 
 

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6  Samuel Pepys Diary
The surname VINES is mentioned 15 times in the diary of Samuel Pepys from 1659 onwards. Dick Vines, G Vines and Mr Vines
are mentioned with regard to card playing. Use the EDIT-FIND facility to search for "vines". 
http://ibiblio.org/gutenberg/etext03/sp85g10.txt
This was soon after Reverend Richard Vines, one of the famed Westminster Divines, died in London; perhaps they were related. 
http://mywebpage.netscape.com/vinesdnastudy/index.html

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7  Mammals Chromosomes
Horse        64 
Przewalski Mongolian wild horse 66 
Donkey     62 
Zebra        44 
Cat           38 
Dog          78 
Fox          34 
Cattle        60 
Goat         60 
Sheep       54 
Pig           38 
Mouse      40 
Chimpanzee, Gorilla, Orangutang  48 
Human      46 

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8  Mutations
Testing of Y chromosome DNA for genealogical purposes measures the number of times that sequences of nucleotide base pairs
are repeated at certain loci or marker positions. For a good explanation of this complex subject see the Contexo web site: 
http://www.contexo.info/DNA_Basics/
The numbers of repeats of sequences of the base pairs in father son lines are very stable over long periods of time, but at any Y chromosome marker a mutation (either a deletion or insertion)  occurs randomly at an average rate of about once in every 500 generations; if 25 markers are checked a mutation may be found every 20 (500/25) generations or say 500 to 600 years. When men who are descended from a common ancestor are tested, the number of mutations they mismatch may be used to estimate the time frame within which their common ancestor was born. 

There is a caculator available for this calculation on the web, courtesy of Ms Ann Turner: 
http://members.aol.com/dnacousins/MRCA.exe
Using 0.002 for the average mutation rate and 25 marker results, we estimate with 95% confidence, (ie high probability,) that a perfect match, 25/25, means there was a common ancestor within 37 generations, and with only 50% confidence within 7 generations.
To tabulate for 0,1 and 2 mismatches: 

                                                     Time Back To Most Recent Common Ancestor 
   Mutations       Probability =  Median (50% Confidence)                     High (95% Confidence) 
in 25 Markers                         Generations           Years                          Within              Years 
      0                                           7                     100                            0 - 37              0 - 550 
      1                                         17                      25                             2 - 57             30 - 850 
     2                                         28                     425                            6 - 75           100 - 1100 

In considering generations in this case one must count those for both men being tested. Thus a perfect match means that with high probability the test indicates the ancestor was born within 37/2 generations multiplied by say 30 years per generation = about 550 years. Using the Turner Calculator a similar table can be made for mutations found in a pair of 12 marker tests. 
The curve for number of generations at 50% confidence limit for various number of markers can be seen at 
http://nitro.biosci.arizona.edu/ftdna/TMRCA.html
 
 

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9  Dominant/Recessive Genes
Every single gene or genetic marker you do have goes back for hundreds and 
thousands of generations. What we're saying is that the chance of inheriting 
a SPECIFIC marker after 6 generations is rather low. Your two copies of that 
marker could have come from any one of the 64 paternal side ancestors you had 
back then, and any one of the 64 maternal side ancestors. 
The concepts of dominant and recessive apply to how the two copies of a gene 
you inherited from your parents interact with each other. For example, the 
genetic hearing loss in my family is a dominant condition. I inherited the
gene from my father, and it doesn't matter how good my mother's copy was -- I 
have the hearing loss. My son has a 50% chance of getting the gene I got from 
my father and 50% from my mother. It turns out that he inherited the one I 
got from my mother, so my father's gene has disappeared completely and none 
of my descendants will have it. You either have the gene or you don't -- it's 
not like the one gene is "diluted" to 50% strength. 

For other recessive conditions, such as cystic fibrosis, you can get a normal 
copy and a defective copy from your parents, and the normal copy can take 
over the function by working extra hard. But if you have defective copies 
from both parents, then you will express the cystic fibrosis disease. Both
parents appear normal, but they are "carriers" without ever realizing it 
until a child is born who happens to inherit the same gene from both parents. 

Ann Turner - GENEALOGY-DNA List Administrator 
10 March 2003 

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