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
CHECK
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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