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If you have taken a BIG Y test to explore and identify your
patrilineal descent back into prehistory, you are among the pioneers of the
latest wave in genetic genealogy. However, you may be able to learn even more
about your line of descent in genealogical times. Chances are that your test
results identified some "Private Variants." These are variants
which so far have only been identified in one man. As soon as they are
identified in others they will become "Named Variants". in the
process it is possible that your own terminal ySNP will be
named and thus extend your trail to your true "genetic coat of arms."
My cousin is shown to have 2
Private Variants
There are
two ways to respond. The passive way is to wait until another person is tested
who also is found to share these variants. The more assertive way is to
identify another man who is likely to share these variants and ask him to test.
In the
case of the cousin whose private variants are shown above, we are currently
evaluating whether to test his son or his nephew when the next DNA test sale
rolls around.
I
recently extended my own terminal ySNP by testing my grandson and then my son
as I described in two earlier blog posts:
In those
posts I described that we discovered my grandson was only a 110/111 ySTR match
with me. Subsequently, we found that my son was a 111/111 ySTR match with me
but he also had one mismatch with his son. So my grandson was the ySTR
mutant!
When it
came to our ySNP analyses, my grandson confirmed my 2 "Private
Variants" but showed one of his own. In so doing one of the previously
private variants became the new terminal ySNP for me. After my son tested, he
confirmed my grandson's private variant, and by so doing, uncovered a new
terminal ySNP that is shared by my son, grandson but not by me. So none of
us currently have private variants but we have two new terminal ySNPs--one
shared by all three of us and one only shared by my son and grandson and
not by me.
I am
advised by Paul Maier, a population geneticist who works for FTDNA that the
ySNP shared only by my son and grandson had multiple possibilities as to when
it was created:
Regarding
your son's mutation of R-FTC50269, what we can say for certain is that it's
absent from your somatic cells (e.g., cheek cells from your swab).
The
mutation could have occurred:
In your
reproductive stem cells (spermalogonia), early during your fetal
developing; those cells made the sperm cell that led to your son;
In one of your
sperm cells later on (after puberty);
Early in the
fetal development of your son, such that both his somatic and reproductive
cells inherited the mutation.
But of
course, you and your son only tested cheek cells, making it difficult to know for
sure which (1, 2, 3) is the case. If you had multiple sons tested and they all
shared the mutation, (1) would be most likely.
In any case, R-FTC50269 would have been
created toward the middle of the 20th century and certainly within the
Genealogical Era. What will you find if you explore your "Private
Variants?"
I'm often asked questions like "what is a 2nd cousin--once removed" and "what is a half=cousin?" The answers all have to do with some simple facts about how you are related to the ancestor(s) you share with your cousin.
The first question you must answer is, how many "g" s are there in the relationship that defines the shared ancestor(s) you have with this cousin?
Are the two of you the same number of generations removed from this shared ancestor?
Do you share a grandparent couple with this individual or do you share only one grandparent in some previous generation?
With the answers to these questions in mind, you are ready to define your relationship with your cousin.
Question #1 is how many "g" s are there in the relationship that defines the shared ancestor(s) you have with this cousin? The most common shared ancestors would be a pair of grandparents. Note that there is one "g" in this the definition of relationship with the shared ancestor(s). Whether it is grandfather or grandmother or a pair of grandparents, there is a single "g" in the term that defines their relationship. Cousins who share grandparents with you are your 1st cousins.
By now you should have noticed all the "g's" sprinkled throughout my prose above. That is deliberate both to draw you attention to them but also to emphasize that they are present in "grandparents" and well as great-grandparents which I shall get to shortly.
If your shared ancestors with the cousin in question are a pair of great-grandparents, this cousin is your 2nd cousin. After all, your common ancestor(s) share 2 g's in their designation. Likewise, if your shared ancestors with the cousin in question is a set of great-great-grandparents, how may "g's" is that? The more astute of you have already concluded that this makes the cousin in question is your 3rd cousin. This pattern extends as far back in your family tree as your research may take you. Just count the number of "g's" and make sure to include the one in grandparents!
Cousin's removed
So far, I've been describing cousins who share the same generation in the family that you do. But as you probably have noticed, many of your closest family members are either a generation older or a generation younger than you. The children of your parents' 1st cousins are your 1st cousins one generation removed. In like manner, the children of your own 1st cousins are also described as 1st cousins one generation removed. These relationships are generally expressed as your "1st cousin--once removed" whether the generation is one generation above you or below you in your family tree.
The same logic continues with additional generations. The grandchildren of your parents' 1st cousins can be characterized as your 1st cousin two generations removed. The mirror image of this relationship would be the grandchildren of your own 1st cousins. They would also be characterized as 1st cousins--twice removed. Again, it does not matter whether or no they are two generations above your or below you in your family tree.
In like manner, the children and grandchildren of your parents' 2nd and 3rd cousins can have the tag of "once removed" or "twice removed" added to their descriptors to help define their relationship to you. Again the mirror image also applies to the children and grandchildren of your own 2nd and 3rd cousins, etc.
While these distinctions may not be necessary for some genealogical studies, often they become important in deciphering relationships based on the amount of shared atDNA (autosomal DNA) shared with a previously unknown individual.
Half cousins
Half-cousins are an extension of the concepts of half-siblings. It occurs when only one half of an ancestral couple is shared by you and your cousin. It can occur at any level of cousin-hood for any number of reasons. For example, if you had a great-grandfather who had 5 children by his first wife and four more by his second, you would be full 2nd cousins with the children with whom you shared a common biological great-grandmother. The children of the other wife would be your half-2nd cousins and would be expected to share about one half as much atDNA as a full 2nd cousin.
Counting your "g s"
Remember to count the "g" in grandparents when counting the degree of cousin-hood.
In the chart above, note that You are located in the box to the right in the row next to the bottom. All those represented in the same row to your left, are your same generation cousins. The one on your immediate left is your 1st cousin; the next one is a 2nd cousin; then 3rd cousin; 4th cousin and 5th cousin on the extreme left. In the bottom row (right to left) are possible 1st cousins -- once removed; 2nd cousins -- once removed etc.
So the answer to the question at the beginning of this blog, "what is a 2nd cousin--once removed", generally would be a person positioned 2 boxes to the left and one down from You in the chart above. If that was your answer, you may be giving a hint to your age. That indicates many of your cousins are younger than you. If you are taking this course for AP credit, you probably figured out that the person 2 boxes to the left of You and one row up would also qualify for this designation. If you caught both, congratulations. You well on your way to becoming a genetic genealogist. Humm. That has two "g s". Maybe 3.
The early ancestors of most of us who have European ancestors just got their 15 minutes of fame this morning thanks to the Nobel Prize awarded to Svante Pääbo.
Press release: The Nobel Prize in Physiology or Medicine 2022
Press release
2022-10-03
The Nobel Assembly at Karolinska Institutet has today decided to award the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo for his discoveries concerning the genomes of extinct hominins and human evolution
Humanity has always been intrigued by its
origins. Where do we come from, and how are we related to those who came
before us? What makes us, Homo sapiens, different from other hominins?
Through his pioneering research, Svante Pääbo accomplished something
seemingly impossible: sequencing the genome of the Neanderthal, an
extinct relative of present-day humans. He also made the sensational
discovery of a previously unknown hominin, Denisova.
Importantly, Pääbo also found that gene transfer had occurred from these
now extinct hominins to Homo sapiens following the migration
out of Africa around 70,000 years ago. This ancient flow of genes to
present-day humans has physiological relevance today, for example
affecting how our immune system reacts to infections.
Pääbo’s seminal research gave rise to an entirely new scientific discipline; paleogenomics.
By revealing genetic differences that distinguish all living humans
from extinct hominins, his discoveries provide the basis for exploring
what makes us uniquely human.
Where do we come from?
The question of our origin and what makes us unique has engaged
humanity since ancient times. Paleontology and archeology are important
for studies of human evolution. Research provided evidence that the
anatomically modern human, Homo sapiens, first appeared in
Africa approximately 300,000 years ago, while our closest known
relatives, Neanderthals, developed outside Africa and populated Europe
and Western Asia from around 400,000 years until 30,000 years ago, at
which point they went extinct. About 70,000 years ago, groups of Homo sapiens migrated from Africa to the Middle East and, from there they spread to the rest of the world. Homo sapiens and
Neanderthals thus coexisted in large parts of Eurasia for tens of
thousands of years. But what do we know about our relationship with the
extinct Neanderthals? Clues might be derived from genomic information.
By the end of the 1990’s, almost the entire human genome had been
sequenced. This was a considerable accomplishment, which allowed
subsequent studies of the genetic relationship between different human
populations. However, studies of the relationship between present-day
humans and the extinct Neanderthals would require the sequencing of
genomic DNA recovered from archaic specimens.
A seemingly impossible task
Early in his career, Svante Pääbo became fascinated by the
possibility of utilizing modern genetic methods to study the DNA of
Neanderthals. However, he soon realized the extreme technical
challenges, because with time DNA becomes chemically modified and
degrades into short fragments. After thousands of years, only trace
amounts of DNA are left, and what remains is massively contaminated with
DNA from bacteria and contemporary humans (Figure 1). As a postdoctoral
student with Allan Wilson, a pioneer in the field of evolutionary
biology, Pääbo started to develop methods to study DNA from
Neanderthals, an endeavor that lasted several decades.
In 1990, Pääbo was recruited to University of Munich, where, as a
newly appointed Professor, he continued his work on archaic DNA. He
decided to analyze DNA from Neanderthal mitochondria – organelles in
cells that contain their own DNA. The mitochondrial genome is small and
contains only a fraction of the genetic information in the cell, but it
is present in thousands of copies, increasing the chance of success.
With his refined methods, Pääbo managed to sequence a region of
mitochondrial DNA from a 40,000-year-old piece of bone. Thus, for the
first time, we had access to a sequence from an extinct relative.
Comparisons with contemporary humans and chimpanzees demonstrated that
Neanderthals were genetically distinct.
Sequencing the Neanderthal genome
As analyses of the small mitochondrial genome gave only limited
information, Pääbo now took on the enormous challenge of sequencing the
Neanderthal nuclear genome. At this time, he was offered the chance to
establish a Max Planck Institute in Leipzig, Germany. At the new
Institute, Pääbo and his team steadily improved the methods to isolate
and analyze DNA from archaic bone remains. The research team exploited
new technical developments, which made sequencing of DNA highly
efficient. Pääbo also engaged several critical collaborators with
expertise on population genetics and advanced sequence analyses. His
efforts were successful. Pääbo accomplished the seemingly impossible and
could publish the first Neanderthal genome sequence in 2010.
Comparative analyses demonstrated that the most recent common ancestor
of Neanderthals and Homo sapiens lived around 800,000 years ago.
Pääbo and his co-workers could now investigate the relationship
between Neanderthals and modern-day humans from different parts of the
world. Comparative analyses showed that DNA sequences from Neanderthals
were more similar to sequences from contemporary humans originating from
Europe or Asia than to contemporary humans originating from Africa.
This means that Neanderthals and Homo sapiens interbred during
their millennia of coexistence. In modern day humans with European or
Asian descent, approximately 1-4% of the genome originates from the
Neanderthals (Figure 2).
A sensational discovery: Denisova
In 2008, a 40,000-year-old fragment from a finger bone was discovered
in the Denisova cave in the southern part of Siberia. The bone
contained exceptionally well-preserved DNA, which Pääbo’s team
sequenced. The results caused a sensation: the DNA sequence was unique
when compared to all known sequences from Neanderthals and present-day
humans. Pääbo had discovered a previously unknown hominin, which was
given the name Denisova. Comparisons with sequences from contemporary
humans from different parts of the world showed that gene flow had also
occurred between Denisova and Homo sapiens. This relationship
was first seen in populations in Melanesia and other parts of South
East Asia, where individuals carry up to 6% Denisova DNA.
Pääbo’s discoveries have generated new understanding of our evolutionary history. At the time when Homo sapiens migrated
out of Africa, at least two extinct hominin populations inhabited
Eurasia. Neanderthals lived in western Eurasia, whereas Denisovans
populated the eastern parts of the continent. During the expansionof Homo sapiens outside
Africa and their migration east, they not only encountered and
interbred with Neanderthals, but also with Denisovans (Figure 3).
Paleogenomics and its relevance
Through his groundbreaking research, Svante Pääbo established an entirely new scientific discipline, paleogenomics.
Following the initial discoveries, his group has completed analyses of
several additional genome sequences from extinct
hominins. Pääbo’s discoveries have established a unique resource, which
is utilized extensively by the scientific community to better understand
human evolution and migration. New powerful methods for sequence
analysis indicate that archaic hominins may also have mixed with Homo sapiens in
Africa. However, no genomes from extinct hominins in Africa have yet
been sequenced due to accelerated degradation of archaic DNA in tropical
climates.
Thanks to Svante Pääbo’s discoveries, we now
understand that archaic gene sequences from our extinct relatives
influence the physiology of present-day humans. One such example is the
Denisovan version of the gene EPAS1, which confers an advantage for
survival at high altitude and is common among present-day Tibetans.
Other examples are Neanderthal genes that affect our immune response to
different types of infections.
What makes us uniquely human?
Homo sapiens is characterized by its unique capacity to
create complex cultures, advanced innovations and figurative art, as
well as by the ability to cross open water and spread to all parts of
our planet (Figure 4). Neanderthals also lived in groups and had big
brains (Figure 4). They also utilized tools, but these developed very
little during hundreds of thousands of years. The genetic differences
between Homo sapiens and our closest extinct relatives were
unknown until they were identified through Pääbo’s seminal work. Intense
ongoing research focuses on analyzing the functional implications of
these differences with the ultimate goal of explaining what makes us
uniquely human.
Key publications
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S. Neandertal DNA sequences and the origin of modern humans. Cell. 1997:90:19-30.
Green RE, Krause J, Briggs AW, Maricic T,
Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF,
Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K,
Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A,
Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ
C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan
Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla
M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D,
Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich
D, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010:328:710-722.
Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 2010:464:894-897.
Reich D, Green RE, Kircher M, Krause J,
Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL,
Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H,
Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV,
Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010:468:1053-1060.
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber
JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R,
Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U,
Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP,
Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012:338:222-226.
Prüfer K, Racimo F, Patterson N, Jay F,
Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C,
Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M,
Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P,
Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL,
Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken
TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B,
Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014:505: 43-49.
>Svante Pääbo was born 1955 in Stockholm, Sweden. He
defended his PhD thesis in 1986 at Uppsala University and was a
postdoctoral fellow at University of Zürich, Switzerland and later at
University of California, Berkeley, USA. He became Professor at the
University of Munich, Germany in 1990. In 1999 he founded the Max Planck
Institute for Evolutionary Anthropology in Leipzig, Germany where he is
still active. He also holds a position as adjunct Professor at Okinawa
Institute of Science and Technology, Japan.
The Nobel Assembly, consisting of 50 professors
at Karolinska Institutet, awards the Nobel Prize in Physiology or
Medicine. Its Nobel Committee evaluates the nominations. Since 1901 the
Nobel Prize has been awarded to scientists who have made the most
important discoveries for the benefit of humankind.
Nobel Prize® is the registered trademark of the Nobel Foundation
Do you have Neanderthal DNA?
23andMe is currently the only major DNA testing company which reports to us information about our Neanderthal DNA inheritance:
"Hey David! You have more Neanderthal DNA than 45% of other customers."
"You inherited a small amount of DNA from your Neanderthal ancestors. Out of the 7,462 variants we tested, we found 236 variants in your DNA that trace back to the Neanderthals."
"All together, your Neanderthal ancestry accounts for less than ~2 percent of your DNA."
"You have one variant associated with being less likely to have a fear of heights.
You have one variant associated with being a better sprinter than distance runner.
You have one variant associated with being more likely to sweat during a workout.
You have one variant associated with being less likely to have a chin dimple."
Read more Neanderthal DNA in Svante's best selling 2014 book: