DNA And Its 4 Main Parts
Understanding Genetic Ancestry
Testing
Back in 1967,
I was very interested in the study of DNA.
By the end of my eleventh year in High School, I knew more about Deoxyribonucleic Acid, (DNA) than my teacher. I wrote a paper on DNA abstraction and
inclusion into other one cell animals that even the professors at Pitt
University could not understand. The
problem: I only could read on a third grade level and could not finish my
work. If I could have, you may have
found me being the father of Genetic Engineering by 1970 instead of Genetic
Corporation in 1976.
Genetic ancestry testing
is the use of DNA information to make inferences about someone’s
"deep" ancestry, hundreds or thousands of years into the past.
Genetic genealogy on the other hand combines DNA testing with genealogical and
historical records, and typically makes use of large databases to identify
matches, or direct comparisons to test for expected matches. There is some
overlap between the two, but genetic genealogy is generally more reliable
because of its use of additional information: the information about your
ancestry available from DNA alone is limited, as we try to explain here.
There are three main types of genetic ancestry
test as explained by MOLECULAR AND CULTURAL EVOLUTION
LAB;
A Y-chromosome DNA (Y-DNA) test provides information about your male line
ancestry only, which in most cultures corresponds with the inheritance of
surnames. Only males carry a Y-chromosome, but a female can learn about her
father line, for example, through her father or brother. Among the tests
currently available there is much variety in the amount of information
provided. The markers tested are of two types: STRs (short tandem
repeats) and SNPs (single nucleotide polymorphisms). These markers have
different mutation rates and so give information at different time
depths. The information you receive depends on which and how many markers
of each type are tested.
SNP testing is used for
deep ancestry purposes to provide information about your haplogroup which tells
you which branch of the Y-DNA tree you belong to. Y-STR tests are used for
genetic genealogy purposes within surname projects to test hypotheses about
patrilineal relationships and to investigate questions about surname origins.
These tests also provide very limited information about your deep ancestry by
giving you a predicted haplogroup assignment.
If two people have the same Y-DNA haplogroup, it means that they
will usually share a common patrilineal ancestor more recently than two people
from different haplogroups, but that common ancestor may still have been a long
time ago. That time can be estimated, but such estimates are not precise with
current standard tests, although comprehensive sequencing of the Y-chromosome
is becoming available and will give improved precision.
The haplogroup
information is often accompanied by a story about the origin of your ancestors,
including a map of the world with arrows indicating ancestral migrations.
Hundreds of thousands of men from around the world have now had their Y-DNA
tested, and we have a very good idea of the distribution of the different
haplogroups in the present-day population. It is, however, difficult to be
confident about where these haplogroups originated and how they spread; many
different histories could explain their current distribution. Sometimes a
company will associate a haplogroup with, for example, Viking, Norman or Saxon
ancestry, but such associations are at best speculative and should be treated
with caution. Just as today most haplogroups are shared among many populations,
so would it have been for past populations. Furthermore, those past populations
would have been genetically diverse, and different from the modern populations
in their regions of origin.
The father line is just
one lineage in your family tree, and as you go further back in time it
represents a rapidly diminishing proportion of your total ancestry. For
example, you have 64 great-great-great-great grandparents, and a man shares his
Y-chromosome with just one of these 64 ancestors.
A mitochondrial DNA test provides information about your female line
ancestry only. Mitochondrial DNA is passed on by a mother to her male and
female children but only females can pass their mtDNA on to the next generation
(males are dead ends for mtDNA). This test, like the Y-DNA test, provides
information about one specific lineage – your mother, your mother’s mother,
your mother’s mother’s mother, and so on back in time. Again the amount of
information provided varies among tests, but the mtDNA sequence is short (just
16,569 DNA "letters") and so sequencing the whole mtDNA genome is
already not very expensive.
An mtDNA test can be
used for genealogical purposes to test a hypothesis about recent female line
ancestry (perhaps arising from genealogical research) or to look for matches in
a genetic genealogy database. The mtDNA test also provides a haplogroup
assignment which may, like the Y-DNA haplogroup, be accompanied by a story and
perhaps a "migration" map. We know a lot about the present-day
distribution of the mtDNA haplogroups, but it is again much more difficult to
make inferences about the more distant past. The mtDNA mutation rate is
relatively high, although there is considerable uncertainty about the precise
rate. The probability of a mutation occurring in the whole mtDNA genome in one
generation (ie, transmission from mother to child) is estimated at between 1%
and 3%. Therefore the time gap between mutations in an mtDNA sequence can be
100 generations or more, and so common mtDNA ancestors cannot be dated
accurately even with full mtDNA genome data: if you share a full mtDNA sequence
with someone, your common matrilineal ancestor could be 1 or 50 generations
ago. For example, it is common for participants in genetic genealogy databases
to have exact full sequence matches with people with ancestry from a number of
different countries.
As with the
Y-chromosome, as you go further back in time your mtDNA represents a rapidly
diminishing proportion of your total ancestry.
An autosomal DNA test provides information from the great
majority of your DNA (the autosomes are the chromosomes other than the X, Y and
mtDNA, and contain most of your DNA sequences, and genes). Although full
genome sequencing is not far away, it remains unaffordable for most and
autosomal DNA tests usually examine up to around 1 million genetic markers
(SNPs) spread across the genome (1 million may sound a lot but there are over 3
billion DNA letters in the human genome, so it's still a small fraction but the
most informative sites are chosen). The markers give information about all your
ancestors in recent generations, but once you go beyond about 10 generations
back into the past (roughly 300 years) only a small fraction of your ancestors
have contributed directly to your DNA: so even if William Shakespeare were your
ancestor (born ~450 years ago), you almost certainly inherited no DNA from
him. This can be a bit confusing: you did inherit almost all your DNA
from ancestors alive at that time, but there are very many of them (perhaps 10
thousand or more), and you only actually inherited your DNA from a few hundred
of them - a small fraction. The others are "pedigree ancestors" but
not "DNA ancestors": you could have inherited DNA from them, but did
not because of the randomness in the 50% transmission of DNA from parent to
child.
The uniparental Y and
mtDNA are exceptions: you inherited them from all your patrilineal and
matrilineal ancestors respectively (the former only if you are male), and so in
a sense they can provide a link with very remote ancestors. But they
represent only a small fraction of your ancestry, and allow only limited
inferences about time depth.
Autosomal DNA tests can be used to identify individuals with
whom you share one or more common ancestors up to a handful of generations in
the past. This is done by looking for large chunks of DNA that you both
share, indicating recent shared inheritance. Sometimes it happens that a
large chunk of DNA is conserved in two individuals from a common ancestor more
than 10 generations in the past, but this is rare: the great majority of common
ancestors at that time depth will not be identified from the DNA of their
descendants today. Although sharing one or more large chunks of DNA makes
it almost certain that the two of you had at least one recent common ancestor,
dating the ancestor(s) is imprecise, particularly beyond about 4 generations
ago. Also the tests have no ability to distinguish certain relationships: for
example, using DNA alone the half-sibling relationship cannot be distinguished
from the grandparent-grandchild relationship, and in the latter case we can't
tell from the DNA which is the grandparent and which is the grandchild.
Algorithms that predict specific relationships are rarely precise beyond 1st
degree, but they can identify more distant relationships approximately, with
good accuracy out to about 2nd cousin, and the precise relationship may then be
confirmed using additional information.
Autosomal tests also
provide information about an individual's "ethnicity" by identifying
sections of the DNA that best match reference databases of modern populations
with geographical or ethnic labels. Ethnicity tests are better called
biogeographical ancestry tests or admixture tests (your "ethnicity"
is a social category that may not accurately reflect your ancestry). However,
the reference populations used for comparison purposes are limited, the ethnic
labels applied to them may be questionable, and they were collected in
different ways for different purposes: they rarely represent true random
samples from a population (e.g. because the "population" itself may
not be precisely defined: populations usually overlap and blend with other
populations). Distinguishing between populations within continents is often
poor with the current resolution of markers and databases. Human genetic
variation usually varies smoothly with geographical distance: as you travel
from Dakar to Vladivostok you can observe continual change in gene variant
frequencies; there is a big genetic difference between start and end cities,
but there are no sharp genetic boundaries along the way.
Ethnic/geographical
assignments have some validity at a large scale. For example in Latin
Americans it is usually possible to distinguish with confidence sections of an
individual's genome that are of sub-Saharan African, European and Native
American origin. However, testing companies will often assign national labels
to genetic clusters, whereas gene variant frequencies tend to change smoothly
across borders. Thus, French people may be assigned a large percentage of
"British" ancestry. Normandy and Kent are genetically similar, as you
would expect from history and geography, so it is not easy to distinguish
English from French based on DNA alone. Given high quality genomic databases it
would be possible to assign an individual to a region of origin with a
reasonable degree of accuracy (human provenancing), but this is beyond what
genetic testing companies currently have available both in terms of having
enough genetic markers in large and well-annotated databases.
As a result of the
random inheritance of DNA, close relatives can often be assigned markedly
different ethnicity percentages. This may be correct. For example
if you have three grandparents from Africa and one from Asia, you and your
brother/sister may receive very different proportions of Asian DNA even though
you share the same parents. However such differences may also reflect
inadequacies in the databases used, or the methods of inference applied.
It is also common to
find that people get very different percentages from different testing
companies. This is partly because each company uses different databases
and the individuals within them are categorised in different ways: there is no
"correct" way to categorise human beings. Each company also uses its
own algorithms to make the estimates, and the target time depth varies from
company to company but is often not explicitly stated. The estimates will also
change over time as additional reference populations are added and as the
algorithms are adjusted or improved.
The Sense About
Science guide Sense about genetic ancestry testing highlights
the limitations of genetic ancestry testing.
Debbie Kennett's blog
post for Sense About Science Sense about genealogical DNA testing provides
an overview of the legitimate uses of DNA testing for genetic genealogy
purposes.
A list of related
articles can be found in the International Society of Genetic Genealogy (ISOGG) website.
We particularly recommend the following:
We particularly recommend the following:
·
Jobling, Rasteiro and
Wetton (2015) In the blood: the myth and reality of genetic markers of identity in Ethnic and Racial Studies(£)
·
"Selling
Roots" by Elliot Aguilar in The New Enquiry.
·
Royal et al. (2010)
"white paper" published by the American Society of Human Genetics
Ancestry and Ancestry Testing Task Force. These authors
say for example that
o
"... moving from
[an] inference of common ancestry to the conclusion that the match implies
something about the biogeographical ancestry of both individuals can be
problematic."
o
"... any
quantitative claims about ancestry should have an easily interpreted assessment
of confidence or accuracy associated with them"
o
"... whenever
formal inferences about population history have been attempted with uniparental
systems, the statistical power is generally low. Claims of connections,
therefore, between specific uniparental lineages and historical figures or
historical migrations of peoples are merely speculative".
·
Bandelt et al. BioEssays (2008).
·
Bolnick et al. Science
(2007). These authors say:
o
"... when an
allele or haplotype is most common in one population, companies often assume it
to be diagnostic of that population. This can be problematic ..."
o
"Many genetic
ancestry tests also claim to tell consumers where their ancestral lineage
originated and the social group to which their ancestors belonged. However,
..."
o
"the tests ...
promote the popular [mis]understanding that race is rooted in one’s DNA"
o
"market pressures
can lead to conflicts of interest".
o
"Lavish but
questionable promises have been made to those who want to trace their genetic
ancestry".
The following lectures
provide a useful resource as an introduction to DNA ancestry testing.
 |
Ancestry testing using DNA: The pros and cons. Public lecture
by Prof Mark G. Thomas at WDYTYA Live at Birmingham's NEC in April 2015. Also
available on youtube
|
 |
DNA for Beginners. Public lecture by Debbie Kennett at Genetic Genealogy Ireland 2014at
Dublin's RDS in October 2014. Also available on youtube
|
http://www.ucl.ac.uk/foi
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