Y and mtDNA are not Adam and Eve: Part 1

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This is going to be the first of a several part (at least two, maybe more, however many it takes) series of posts discussing both the science and the science communicating regarding a recent paper:

Science. 2013 Aug 2;341(6145):562-5. doi: 10.1126/science.1237619.

Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.

First, you should go read it. It is short and sweet, and, yay science!

What I’m going to talk about first is how this paper relates to communicating science. Future posts will expand and elaborate on the research. I’ll also note that I am not picking on this paper alone, because several other scientific papers have done the exact same thing. This one is just the most recent incident, and, more personally,  I was actively involved in trying (and failing) to prevent the miscommunication. As such, I feel the need to provide more explanation.

The recent paper did an excellent job of publicizing itself. It has a sexy title, and it mentions, “Adam and Eve” in the main manuscript:

“Dogma has held that the common ancestor of human patrilineal lineages, popularly referred to as the Y chromosome “Adam,” lived considerably more recently than the common ancestor of female lineages, the so-called mitochondrial “Eve.”

Regardless of the results (which are definitely new, and we’ll discuss later), these things alone would get it a lot of press. They are tangible ideas that the public can relate to, and make it easy for a science journalist to build a story around.

But, they are also extremely misleading. I think they are also harmful, in the long-term for educating and communicating with the public.

I was interviewed by two different science writers to comment on this paper, and in both interviews I stressed how inappropriate the “Adam Y” and mitochondrial or “mtDNA Eve” analogies are. You can see how well they took that into consideration: here and here. I really enjoyed talking with the journalists, so hope they won’t think I’m picking on them either because, to be fair, nearly every popSci article used this analogy (see here, here, here, and here). I’ll take a sentence here to especially note the article by Francie Diep, here, that took a different approach.

While I have several reasons to disliking this analogy, I cannot fault the journalists completely for using it in this instance. Aside from my protests, there is no reason science journalists should think that it is a bad analogy, because it was used in the manuscript (without context or explanation).

Okay, so I’m upset that the paper would reference the “Y Adam” and “mtDNA Eve” without explaining them, but why are these analogies wrong? The public connects to them - they are visual and engaging, so what’s the problem?

First, a little background:

Who are Adam and Eve?
If you are not familiar with it, in the Old Testament, one of the creation myths is that God created a man (Adam) and a woman (Eve), and all other humans are descended from this pair of first humans.

Simple enough.

What are the Y and mtDNA?
Each person has half of their DNA from their genetic father (who provided the sperm) and half of their DNA from their genetic mother (who provided the egg).

The Y chromosome passes through the genetic male lineages (genetic males are XY, inherit their Y chromosome from their genetic father, and will pass it on to their genetic sons).

The mtDNA is a small circular piece of DNA that all of us have in our cells, but is only transmitted through the genetic female lineage (the egg contains the mtDNA, so although genetic sons and daughters both receive this mtDNA, only the genetic female lineage makes eggs, so mtDNA is only passed on by daughters).

The Y and mtDNA are unique
Unlike the autosomes, which come in pairs (one copy from genetic mom, one from genetic dad), and can swap DNA, resulting in the mixing up of information from genetic mom and dad, neither the the Y chromosome nor the mtDNA have a partner (Y only from genetic dad, mtDNA only from genetic mom). So, it is somewhat simpler to trace these two pieces of DNA back in time.

Using some math and observations of the numbers of observed changes (mutations) on the Y chromosome and the mtDNA, scientists can estimate how closely related any two Y chromosome, or any two mtDNA are, and when they last shared a common ancestor.

What’s the problem with “Y Adam” and “mtDNA Eve”?
If we can estimate the most recent common ancestor of the mtDNA and the most recent common ancestor  of the Y chromosome, isn’t this kind of like the creation story of Adam and Eve?

No.

There are several reasons people don’t like these analogies, but in my opinion there are two overwhelmingly wrong ideas that get propagated when using them. Applied to genetics, using the creation story of “Adam and Eve” to describe the most recent common ancestor of the Y and mtDNA, respectively, implies that:

Bad analogy #1: There were only two humans alive at that time.

There were several other genetic females living at the time of the person who carried the mtDNA ancestor of us all, and several other genetic males living at the same time as the genetic male who carried the Y chromosome ancestor of modern genetic males.

Bad analogy #2: Y “Adam” knew (presumably intimately) mtDNA “Eve”.

Just because the person who carried the ancestral Y chromosome is predicted to live about the same time as the person who carried the ancestral mtDNA (120,000-156,000 years ago for the Y lineage versus 99,000-148,000 years ago for the mtDNA lineage), in no way suggests that they lived at exactly the same time. Although it is short on an evolutionary time scale, those are pretty big time ranges when you’re thinking about a human lifespan! Further, even if they happened to live at the exact same time, there is no evidence that they were located in the same region or would have interacted at all.

These two erroneous assumptions stem directly from using the “Adam and Eve” analogy. The public is smart, and while they may not have the vocabulary (heck, people outside of our specific sub-disciplines do not share the same vocabulary), they can understand analogies. When we, as scientists, supply an analogy that doesn’t accurately describe the research, it is not the public’s fault for misunderstanding the work; it is our fault for misrepresenting it.

There is no reason why the “Y Adam” and “mtDNA Eve” should have been mentioned in the primary manuscript, but if it was necessary, it should have clearly been explained why this analogy is not appropriate.

Well, that’s a start.

In the follow-up posts I will go into:
1. More detail describing bad analogy #1 and #2 above, and misunderstandings relating to the title
2. An accessible research summary of the actual paper (yay! - This really is the most fun part.)
3. Addressing questions you all have about this topic!

So, stay tuned!!

56 Comments

I was just thinking that a relatively homogenous initial population would give the same result, but of course, that population had to come from somewhere…

This bad analogy give aid and comfort to the Ray Comforts of the world - and other creationist charlatans as well.

More importantly, it confuses well-meaning people.

This would be a great paper to use for discussion in my non-majors biology course, specifically to address the misconceptions that you highlighted in using this analogy. I usually try to avoid using analogies because so many of them either carry misinformation depending upon the background of the student reading/hearing it or they fail to penetrate because the analogy is to something unfamiliar to the student. Personally, I would avoid analogizing altogether on this one but I was wondering if you would be able to suggest a good analogy to replace the Adam/Eve one for this example?

Presumably, not even the entire Y chromosome came from a single individual, since there’s still a little crossing-over (with X) occurring even there, as I recall.

Considering that could lead to the impartation of some knowledge of what a “Y Adam” can mean–as well as about the evolutionary origin of the Y chromosome.

Glen Davidson

Thanks for this. It is indeed difficult to get people to understand what the actual evidence says when using terms such as Adam and Eve. It is little wonder that people can get confused.

After getting the real scientific interpretation across, the next important message to communicate is the this is absolutely NOT evidence for the biblical Adam and Eve, indeed it is extremely strong evidence against that hypothesis, as if any more were needed.

I guess, for this, I would probably avoid analogy, and just talk about how cool it is that we can trace these lineages back in time (because they do not recombine). I’m working on a video to explain the concept of the mtDNA ancestor - hoping to finish it up tomorrow or Thursday - will post here.

I remembered reading here a long time ago something about how Y-Adam and mt-Eve are not really all that special. Every gene can be similarly followed back through its own separate lineage, and will eventually resolve to a (different) common ancestor. Y-Adam and mt-Eve are the ones talked about only because their lineages are passed down through a single sex, and are thus easier to work with than any of the others.

It took me a bit of searching (it was much further back than I’d thought), but I’m pretty sure that it was this PT entry that I remember. The url it links to doesn’t work any more, but a quick search turned that up too, here.

It seems to me that, since the 2nd Genesis Story’s bit on Adam and Eve is MYTH, the use of the as allegory doesn’t matter. Yes, if they were real people, or if the original authors had intended them as real people, then they actually did have sex, and this would be all confusing. But they weren’t. They’re myth, to illustrate a deeper point. So I’m not getting why they would be a bad use for analogy for the public to pin something on to understand the further science. Perhaps someone could explain it further to me.

It seems to me that Y-chromosomal Adam is not Adam at all but Noah. Noah is the last common ancestor of all living males (according to the myth), not Adam. The Hebrew Bible says clearly,

And Noah went in, and his sons, and his wife, and his sons’ wives with him, into the ark, because of the waters of the flood [Genesis 7:7]

and repeats the same information in verse 13. Now Noah was (presumably) the father of his sons, but he was (presumably) not the father of his daughters-in-law. Thus, Mitochondrial Eve is not Noah’s wife, but Mitochondrial Adam is Noah, not Adam. Noah and Eve did not live at nearly the same time, incidentally, and they never met.

Jedidiah said:

It seems to me that, since the 2nd Genesis Story’s bit on Adam and Eve is MYTH, the use of the as allegory doesn’t matter. Yes, if they were real people, or if the original authors had intended them as real people, then they actually did have sex, and this would be all confusing. But they weren’t. They’re myth, to illustrate a deeper point. So I’m not getting why they would be a bad use for analogy for the public to pin something on to understand the further science. Perhaps someone could explain it further to me.

Nowhere in my post do I say that the analogy is bad because it is related to the Bible. It is a poor analogy because it leads to misunderstandings (namely that there were only two humans alive at the time, and that they knew each other/procreated together).

Matt Young said:

It seems to me that Y-chromosomal Adam is not Adam at all but Noah. Noah is the last common ancestor of all living males (according to the myth), not Adam. The Hebrew Bible says clearly,

And Noah went in, and his sons, and his wife, and his sons’ wives with him, into the ark, because of the waters of the flood [Genesis 7:7]

and repeats the same information in verse 13. Now Noah was (presumably) the father of his sons, but he was (presumably) not the father of his daughters-in-law. Thus, Mitochondrial Eve is not Noah’s wife, but Mitochondrial Adam is Noah, not Adam. Noah and Eve did not live at nearly the same time, incidentally, and they never met.

Matt, I’m confused. Why try to explain it in Biblical terms at all?

Why try to explain it in Biblical terms at all?

1. Just for fun. I did not try to explain anything in Biblical terms, but only noted for anyone who wants to tie the research to the Bible that they will never get back to Adam anyway, only to Noah.

2. Much of the narrative portion of the Bible is arguably true (at least if you do not think that All Is Archeology), and it is interesting to figure out which. I do not for a minute think there were an actual Adam and Eve - the names are too cute, for one thing - but there were doubtless a helluva lot of floods in that area, and maybe some tribe actually had an ancestor called Noah, who lived on a houseboat and survived an especially big flood.

It is a matter of no importance - just fun reading the Bible like a Communist apparatchik and seeing what you can come up with. I think what I have just come up with precludes a Biblical literalist from saying that Y-chromosomal Adam is Adam.

Sorry if this is stream of consciousness, but I am tired.

M. Wilson Sayres said:

Nowhere in my post do I say that the analogy is bad because it is related to the Bible. It is a poor analogy because it leads to misunderstandings (namely that there were only two humans alive at the time, and that they knew each other/procreated together).

M Wilson- yes, I wasn’t thinking that you were rejecting it just because it was the Bible. I guess though, my thought is that since the original author/s clearly intended it as myth, their intention was never that this be perceived as one man, one woman. As Matt alludes to, the names themselves are clear archetypes- well, clear to everyone but 20th/21st century Americans. They represent groups- not even that. They represent ideas. It seems to me therefore that Adam and Eve are ideal for use as mDNA and Y, since they represent an idea. The only problem is this strange offshoot of Christians in America who think that Adam and Eve are real people, and thus their faulty interpretations of the text cause confusion. Of course, those are exactly the type of people we need to reach if we are hoping to convince these last anti-evolution holdouts.

As a non-scientist I actually like the use of the terms mitochondrial Eve and Y-chromosomal Adam so long as they are properly explained. It needs to be made clear that there is no correlation with the Biblical Adam, we are referring to two specific lineages, and that “Adam” and “Eve” did not live at the same time. The problem is with the press who always tend to over-simplify everything.

On another matter why did this paper ignore the finding of haplogroup A00 published back in February this year in the American Journal of Human Genetics which places the root of the Y-tree at around 338,000 years ago? http://www.cell.com/AJHG/abstract/S[…]7(13)00073-6

The full text can be found here:

http://haplogroup-a.com/Ancient-Root-AJHG2013.pdf

While I have several reasons to disliking this analogy, I cannot fault the journalists completely for using it in this instance. Aside from my protests, there is no reason science journalists should think that it is a bad analogy, because it was used in the manuscript (without context or explanation).

While your frustration over the Adam and Eve terminology is understandable because of the confusion it can cause, I think you are being a little harsh on the authors, and a little naive about their influence on journalists’ use of the Adam and Eve terminology. The passage you quote with the Adam and Eve reference (repeated below) comes in the last paragraph of the paper and does not at all appear to be a gratuitous reference that exploits or advocates for those labels. Rather, with the qualifiers “popularly referred to” and “so-called”, they appear simply to be making explicit that the subjects of their research are equivalent to what have long been popularly known by those labels. That seems like proper context to me. And given that the Adam and Eve terminology has been ubiquitous and pervasive for 25 years, I think it would be folly to think that, had the authors refrained from using those terms in their last paragraph, science journalists wouldn’t have known about or applied those labels anyway. In fact, I’d bet that if the article had not mentioned the terms Adam and Eve, the first question that a good science journalist would have asked the authors, in fact I’d assert should have asked, would be, “So, just so I’m clear on this, the common ancestors you’re talking about are the same as those that others have referred to as “Y Adam” and “Mitochondrial Eve”, right?” The genie of that terminology is long out of the bottle, is it not?

Dogma has held that the common ancestor of human patrilineal lineages, popularly referred to as the Y-chromosome “Adam,” lived considerably more recently than the common ancestor of female lineages, the so-called mitochondrial “Eve.”

Why try to explain it in Biblical terms at all?

“Adam and Eve” are, like it or not, deeply embedded into our culture, our thought, and our subconscious. Deeply.

Just because the Protestant Bible isn’t literal doesn’t mean it’s worthless. It is beautiful poetry. And the Adam and Eve Myth is a big part of that beauty.

That’s why.

“Observations of the numbers of observed changes(mutations)” Thats the problem with the whole business here. Not misdirection of information. These observations say nothing of what could of happened in the DNA . Its just a line of reasoning nothing did/could happen and so extrapolation backwards produces these results. I don’t mean welcome mutations but other mechanisms to affect DNA change and so physical change.

Anyways this creationist sees this as a welcome new data. it does place generally the Adam near the Eve even with your time and place points. It leads toward the idea of a first mand and woman from whence we all came. Thats the welcome thing creationists can rightly pick up on. As long as they point out its coming from those with evolutionary presumptions and time presumptions. It is probably a unwelcome fact to evolutionists dealing with the public on origin issues.

Same kind of confusion arises when one talks about the Higgs (God) particle and other instances in science where either the authors implicitly bring up the societal myths or journalists embelish the story/ies with their lack of scientific knowledge, hoping to sell more copy or thinking they’re are simplifying the concept.

Thanks M. Wilson for the explanation. In my experience, the bad terminology does indeed create a lot of confusion, and it’s frequently used by some creationist factions to argue for a literal Adam and Eve (much more frequently than some people here think). Dennis Venema, from the Biologos Foundation, explains the concepts very well with nice graphs, in the following article: Mitochondrial Eve, Y-Chromosome Adam, and Reasons to Believe. I hope that you make use of similar graphs in your upcoming video/series of articles. They are really helpful. I hope that you do a short review of the evidence for past population sizes as well.

I have a small question for you: Is there a way, based on the data available (or the data that might become available), to rule out that possibility that the mtDNA MRCA met with the Y chromosome MRCA? You don’t have to answer that here. I hope that you throw some light on that in your upcoming articles. Thanks!

This is Rhazes again with a different account, sorry for the confusion. Can you please also comment on the main finding of the study? Was resolving the discrepancy really necessary or required in the first place, given our understanding of genetics and the human mating system? In other words, if it turns out that there’s a real “discrepancy in time to common ancestor of males versus females”, does that pose any theoretical problems? I remember watching an old video about the subject, and the explanation for the discrepancy that the presenter gives made sense to me. And the video is by the way a testimony to how confusing and misleading the terminology is. I hope that you comment on this point as well. Thanks!

I think there were two typos in this very good article. You said:

There were several other genetic females living at the time of the person who carried the mtDNA ancestor of us all, and several other genetic males living at the same time as the genetic male who carried the Y chromosome ancestor of modern genetic males.

But it should have said (putting the corrections in italic):

There were several thousand other genetic females living at the time of the person who carried the mtDNA ancestor of us all, and several thousand other genetic males living at the same time as the genetic male who carried the Y chromosome ancestor of modern genetic males.

.…as the effective population size of the human population at that remove in time was about 10,000 so there would have been about 5,000 of each sex.

What fraction of the time would “Eve” come from the same generation as “Adam”? Imagine yourself tossing a pair of coins simultaneously with Heads probability p for each. Do so repeatedly until at least one coin comes up Heads. What fraction of the time does the first pair of tosses that has a Heads have both coins coming up Heads? I make it out to be p/(2-p). p being 1/(N/2), we get 1/(N-1).

Now if they do happen to come from the same generation, what fraction of the time would they come from the same mated pair? If there are N/2 mated pairs, which is a bit too neat, that chance would be the reciprocal of this number, 2/N (“Eve” come from one of these pairs. What is the chance that “Adam” comes from the same mated pair?).

So the overal chance that they come from the same generation and the same mated pair is 2/(N(N-1)) or 1/49,995,000, so slightly more than 1 in 50 million.

A correction. The calculation I just gave was for a pair of Y lineages and a pair of mitochondrial lineages going back in time. But there would start out to be many more, and only back a ways would the ancestry thin out to a pair. So the calculation is more complex, but in any case the chance that “Eve” and “Adam” were a mated pair is very small, one part in tens of millions.

Question: Was there also an ancient ‘Australopithecus Adam and Eve’, a ‘Lemur Adam and Eve’, a ‘Lobed Finned Fish Adam and Eve’, etc.?

Most eukaryotes (and all multicellular organisms) have mitochondria. For those that also have a Y chromosome that is (mostly) not recombining with the X chromosome, there would be a mitochondrial Eve and a Y chromosome Adam.

But it goes further than that. We have a similar coalescent ancestor for every small piece of our genomes. However they are randomly either females or males, since those lineages go back through both males and females. Thus we have Cytochrome C Sam, Hemoglobin Beta Harriet, and a host of others, maybe 100,000 of them in all. Most of those are hundreds of thousands of years earlier than “Adam” and “Eve”, as autosomal genes coalesce four times as slowly as Y’s or mitochondria. So Malate Dehydrogenase Molly was possibly not a Homo sapiens.

And the lungfish and fungi also each have their multitude of coalescent ancestors of different parts of their genome.

We should give names to all the original ancestors of each chromosome, chosen to correct this misunderstanding.

For example, chromosome 2 is a fusion of ape chromosomes 2a and 2b. So we should give the ancestors of those two chromosomes names like Bonzo and Curious George.

“Steve” should be the official name of the ancestor of a chromosome; let’s say chromosome 3. Let’s make the religious right talk about how we all come from Adam and Steve.

If you don’t know the gender of the ancestor, give them gender neutral names like Tracy.

We should pick some names from other mythologies and cultures, e.g. the ancestor of all Chinese is the Yellow Emperor, etc.

According to Wikipedia, “Y-chromosomal Aaron is the name given to the hypothesised most recent common ancestor of many of the patrilineal Jewish priestly caste known as Kohanim”.

diogeneslamp0 said:

We should give names to all the original ancestors of each chromosome, chosen to correct this misunderstanding.

For example, chromosome 2 is a fusion of ape chromosomes 2a and 2b. So we should give the ancestors of those two chromosomes names like Bonzo and Curious George.

“Steve” should be the official name of the ancestor of a chromosome; let’s say chromosome 3. Let’s make the religious right talk about how we all come from Adam and Steve.

If you don’t know the gender of the ancestor, give them gender neutral names like Tracy.

We should pick some names from other mythologies and cultures, e.g. the ancestor of all Chinese is the Yellow Emperor, etc.

As for the gender neutral name, I vote for Pat.

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

Some in the Citizen Genetic Genealogy community actually prefer working with either Y-DNA - mtDNA - or both versus Autosomal DNA.

And yes, we are not some kooks wanting to trace our lineages back to a putative ‘Y-DNA Adam” or a ‘mtDNA Eve’ a couple hundred thousand years back. Most of us happy getting back 500 to 700 YBP to the 1300s and 1400s.

A case in point is Dr. John Ashdown-Hill who went back 17 generations to the Ibsen family to locate a mtDNA J1c2c with King Richard III who died in 1485. Ashdown-Hill is a professional freelance historian and a remarkable Citizen Genetic Genealogist. However, the University of Leicester is embarked on a PR campaign to airbrush Dr. John Ashdown-Hill out of the picture and to give near 100% of the credit to the university geneticist, Dr. Turi King, as well as others at the university. see: http://www.thisisleicestershire.co.[…]xzz2bJvIkPSF see: http://en.wikipedia.org/wiki/Exhuma[…]I_of_England

Now, we have persons such as Razib Khan at the Gene Expression blog saying: Please ignore mtDNA and Y chromosomal haplogroups http://blogs.discovermagazine.com/g[…]haplogroups/#.UgK1w5K1GAA

“This is a public service announcement. If you are a user of direct-to-consumer personal genomics services, please do not pay any attention to your mtDNA and Y chromosomal haplogroups.” “What you should pay attention to are your autosomal results”

Khan also supports the views of Dr. Mark Thomas who refers to Citizen Genetic Genealogists as “Genetic Astrologers”

Khan is an outspoken and often incompetent antagonist to Consumer Genetic Genealogists. He fancies himself as knowing a little about everything when the cold hard facts that he mainly parrots the works of others and spouts off his widly conservative views.

So, I hope that the Pandas Thumb blogger will support the works of Citizen Genetic Genealogists and offer constructive comments on how we can up our game.

https://www.google.com/accounts/o8/[…]7Qc2Onc5o5QY said:

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

What is it that you’re not buying? The existence of a most recent common mitochondrial genome or Y-chromosome ancestor is simply a by-product of genealogical descent. AFAIK, these concepts do not suggest that the current mitochondrial “eve” lived during an extreme bottleneck. In all likelihood, this individual (or more specifically, her mitochondria) was a member of a much larger population.

I agree: what does it mean that “a homogenous population was being evolved”?

As far as the efforts of people to trace ancestry through Y and mitochondria, what is the objective? The rest of their genes come from lots of sources.

I wonder what one gets from knowing that a Famous Person had my Y chromosome. Suppose mine was identical to Richard III’s. Good conversation, but so what? Are those 13 protein coding loci giving us important insight into my imperious behavior?

The usefulness of any of these coalescent studies is much less in the specific genealogy, than it is in insights it gives into past population sizes, migration rates, mutation rates, population growth rates, and recombination rates. Particular genealogies will vary enormously from one region of the genome to another, and also be hard to infer precisely. But we can use Markov Chain Monte Carlo sampling to average information over our uncertainty about the genealogy, and accumulate information about those genetic parameters and population parameters. Knowing that I am the 28th-removed grandnephew of Count Otto the Gross is much less useful.

I think this stems from the bad analogy. As others have pointed out, we can trace back to the shared ancestor of any genomic region (we might have to get smaller and smaller on the autosomes), but there is no one person whose genome was the ancestor of all of the chromosomes (1-22), X, and either mtDNA or Y.

I think it’s as was already said above - once a term is established in popular usage, it ain’t gonna change because somebody thinks that’s the thing to do.

Language isn’t intelligently designed, either. (As long as nobody mentions “Esperanto”, anyway… :D ).

Then there’s the “Big Bang”…

I note that somebody already mentioned “God particle” above.

Henry

Alright. I’m feeling really dense here. But I’m a computer science guy, so I’m used to that feeling. I worked hard to get to the AHA(!) point that populations evolve, not individuals, and that evolution and speciation “events” are like the threads of a slow river meandering through a flood plain, splitting, combining, and splitting again until eventually finding separate courses. So, what’s with this whole mitochondrial Eve thing? Is this notion really saying that all living women descended from a single human female? I get the idea that “mtDNA Eve” lived in a group of people, and the idea that if you trace things back you get to a single ancestor. But isn’t that “single ancestor” way, waaay, waaaaaay before the first mammal, let alone the first hominid? If Eve lived among a group of people, did all those other women contribute nothing to the gene pool? All those other lineages simply died out? People are talking like this whole notion is completely obvious. I don’t see how it’s “obvious”.

What am I missing?

Scott F said:

Is this notion really saying that all living women descended from a single human female? I get the idea that “mtDNA Eve” lived in a group of people, and the idea that if you trace things back you get to a single ancestor. But isn’t that “single ancestor” way, waaay, waaaaaay before the first mammal, let alone the first hominid? If Eve lived among a group of people, did all those other women contribute nothing to the gene pool? All those other lineages simply died out?

The post I’m working on now addresses, conceptually, the TMRCA, but it also touches on this issue. The title referring to the common ancestor of “males and females” is completely misleading.

Continuing with the mtDNA theme here:

Yes, we can identify a common ancestral mtDNA. The person who had that mtDNA also had a whole genome (chr1-22, XX). The rest of her genome was not “ancestral”, and definitely many of her contemporary genetic female companions passed on their autosomal DNA, just not their mtDNA.

Scott F said:

What am I missing?

If my layman’s reading counts for anything, the LCA is simply an artifact, a necessary consequence of any digital inheritance system. For any essentially discrete heritable element (a gene, a mitochondrion, or I suppose even a whole bacterium if you could discount lateral transfer), eventually the lineage of one individual will dominate and all of the others will dead end.

The amount of time necessary for this to occur is highly variable, and isn’t directly related to the evolutionary history of the organism as a whole (except perhaps in the case of clonal reproduction). As one of the comments in the thread I linked to before mentions, every time an individual dies there’s a possibility of the actual individual ancestor changing, since that death could mean the end of a specific sub-lineage.

It also depends on the total population you’re looking at. If you took humans and chimpanzees together, then the mt-LCA would (I guess) have to have lived millions of years ago, before either species even existed. But I imagine the mt-LCA of chimpanzees alone would probably be much younger than that of humans, due to the smaller population size.

Of course I could be wrong. Someone please correct me if I am.

https://www.google.com/accounts/o8/[…]7Qc2Onc5o5QY said:

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

This comment apparently comes from a troll, but it does accidentally raise some good areas for clarification. (How do I know it probably comes from a troll with evidence-independent pre-set biases that can’t be reached with logical persuasion? First of all the language - “Nope, sorry, not buyin’ it”. Now, I might well say those exact words in some different context, but in a scientific discussion they come across as somewhat juvenile, hostile, and pseudo-“folksy”. Second of all, the “homogenous population was being evolved” bit. Science-y words with no apparent meaning. Of course, I could be wrong - maybe the writer will clarify with a reasoned response.)

Having said that, discussion of the most recent common ancestor of a gene does imply, not assumptions, but operational definitions.

If my mother has a new polymorphism (and she undoubtedly has dozens to hundreds), we could define that as a new gene. If my brother inherits that polymorphism (50% chance if it’s autosomal) and goes on to have many descendants, then my mother was the “particular polymorphism Pam” (no, her real name isn’t Pam) for that polymorphism. If there was a medical or legal significance to that polymorphism, its descent might actually be traced.

We define “Homo sapiens” in a variety of ways, mainly anatomic, relative to other hominids.

What’s interesting about us is that our species, as reasonably defined, did explode to a very high biomass in a very short period of time (by evolutionary standards), from an initially small population. Therefore, if we look for “Y chromosome Adam” we get a somewhat meaningful result, which fits with prior predictions about human populations based on other evidence. “Cytochrome C Sam”, on the other hand, would have been a single celled organism that lived a very, very long time ago. As it happens, the emergence of a genetic sequence that can meaningfully be called a cytochrome C gene is a fascinating and important question, but probably something that cannot be pinpointed with the (relatively) high precision with which we can place a time frame on “Y chromosome Adam”.

Genetic “Adam” and “Eve” were each part of a larger population, and many members of that population ALSO contributed genetic material that modern humans carry (because they shared many alleles), just not the particular genetic material that these studies focus on. If you trace back certain elements of the Y chromosome, those particular genetic elements can be traced back to a particular individual, at a point in time which is consistent with other evidence about the history of the human race.

You could say it’s arbitrary to focus on these particular genetic elements. However, an implied goal here is a correlation with physical anthropology and paleontology. These genetic elements allow us to trace “direct” ancestry in a highly analogous manner to traditional genealogy.

Does this mean the Y chromosome (and only the Y chromosome) of everybody alive today has descended from a single individual that lived 120K-156K years ago; but we share other chromosomes contributed by others in that ancient population?

And similarly for the mitochondrial DNA?

I think I understand the sources of confusion here thanks to the post, but I am wondering what the larger point or lesson of this research is. What does finding the LCA of a particular piece of genome tell us? Why is it important to find the Adam and Eve of these particular bits of DNA, if as it seems they are selected for ease of tracing?

Hmm… Okay. So, the “Y Adam” and the “mtDNA Eve” are different individuals at different points in time, because you are not talking about the single ancestor of all men or all women. You’re talking about the single ancestor of just one piece of the DNA. Another example one might pick is the Human Chromosome-2 fusion. It seems to me most likely that such a fusion event could have happened in exactly that way only once. For a period of time, the fused chromosome could still viably interbreed (if that’s the right notion) with the rest of the ancestral population, enough so that this chromosome mutation spread to the rest of the population. And it didn’t have to spread to all of the population, just the part that eventually split to become “human”. But this means that there was one individual who was the ancestor of the chromosome-2 fusion site that everyone now carries.

Is that the idea?

Carrying the “river” analogy further, and mixing metaphors, if the evolving population is the branching river, one could imagine the river as made up of lots of individual threads, each thread representing a gene, or some distinct characteristic of the DNA. If one were to try and follow one of these threads, you would follow a particular path through the streams and tributaries of the branching river. If you were to then follow a different thread, it would follow a different path through the historical waters.

Then, each individual is at a particular fixed point in the river, and each individual represents a particular bundle of these threads at a particular point in time. Each thread can be followed (conceptually) through different sets of individuals. No single individual would ever contain all the possible threads (unless there really was a single, historical “Adam”, or “Noah”), even though a single individual thread must have had its start inside one individual.

This, I think, directly addresses the question of, “How did the first male with mutations WXYZ meet up with the first female with mutations WXYZ?” It’s a different perspective on how a single mutation can spread through a population. If you start with a single spontaneous mutation, it’s not too difficult to grasp the concept that it could spread through the rest of the population (through genetic drift, if nothing else), even if that exact same mutation never spontaneously appeared in any other unrelated individual. But turn that around, look at it from the other direction of time, and it’s more difficult to imagine that some mutation that everyone shares (is it really a “mutation” if everyone has it?) must have originated with a single individual.

Even if all that were “true” in some metaphorical sense, it only helps understand the “Y Adam”. It doesn’t help as much with the “mtDNA Eve”. Unlike the rest of the genes (including the “Y”), the mitochondrial “clump” of DNA doesn’t “mix”. Wouldn’t the least-common-ancestor of the mitochondria be the first eukaryote to swallow the first proteobacteria? Isn’t that the point where that particular “thread” started? If the other females at the time contributed any genetic material to today’s population, they must also have contributed their particular version of the mitochondria. Mustn’t they?

Scott F said: Even if all that were “true” in some metaphorical sense, it only helps understand the “Y Adam”. It doesn’t help as much with the “mtDNA Eve”. Unlike the rest of the genes (including the “Y”), the mitochondrial “clump” of DNA doesn’t “mix”. Wouldn’t the least-common-ancestor of the mitochondria be the first eukaryote to swallow the first proteobacteria? Isn’t that the point where that particular “thread” started? If the other females at the time contributed any genetic material to today’s population, they must also have contributed their particular version of the mitochondria. Mustn’t they?

IANAB… I think of it this way…

You have a population of many females. Each will pass her unique version of mtDNA to her children. Allowing for mutations, her female children will pass their versions all to their children.

Not all females will have children, and of those that do, not all will have female children. Over time, any unique lineage of mtDNA can go extinct. Eventually, you will get a branching tree structure of related patterns of mtDNA traceable back to a single ancestral form. The earliest ancestress of the remaining traceable form becomes the “mtDNA Eve”. As various modern lineages of mtDNA go extinct, the “mtDNA Eve” will change.

Some one with good biological chops will be able to tell if I’ve got the concept down reasonably correctly for a layman.

david.eugene.carlson said:

https://www.google.com/accounts/o8/[…]7Qc2Onc5o5QY said:

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

What is it that you’re not buying? The existence of a most recent common mitochondrial genome or Y-chromosome ancestor is simply a by-product of genealogical descent. AFAIK, these concepts do not suggest that the current mitochondrial “eve” lived during an extreme bottleneck. In all likelihood, this individual (or more specifically, her mitochondria) was a member of a much larger population.

You can trace one allele of one locus back to a common individual, or a shared haplotype, but you can’t trace an entire mt, or y, genome back to one common individual.

W. H. Heydt said:

IANAB… I think of it this way…

You have a population of many females. Each will pass her unique version of mtDNA to her children. Allowing for mutations, her female children will pass their versions all to their children.

Not all females will have children, and of those that do, not all will have female children. Over time, any unique lineage of mtDNA can go extinct. Eventually, you will get a branching tree structure of related patterns of mtDNA traceable back to a single ancestral form. The earliest ancestress of the remaining traceable form becomes the “mtDNA Eve”. As various modern lineages of mtDNA go extinct, the “mtDNA Eve” will change.

Some one with good biological chops will be able to tell if I’ve got the concept down reasonably correctly for a layman.

IANAB as well …

I find your treating of the subject perfectly sufficient. Especially the part that “mtDNA Eve” has probably changed (maybe several times) during the last 50 000 years.

One might think that this description leads always to one individual (which might change). That is not so in general (although it might be true in a special case). The set of the features common to the mtDNA of all now living humans was most probably shared by more than one individual.

harold said:

https://www.google.com/accounts/o8/[…]7Qc2Onc5o5QY said:

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

Of course, I could be wrong - maybe the writer will clarify with a reasoned response.)

Having said that, discussion of the most recent common ancestor of a gene does imply, not assumptions, but operational definitions.

Reasoned response to unreasonable insult? Of course. The topic isn’t ancestry of a gene. It’s ancestry of a genome.

https://www.google.com/accounts/o8/[…]7Qc2Onc5o5QY said:

Nope. Sorry. Not buying it. Heuristic hyarchical clustering algorithms that work down to one individual have assumptions built in. Still makes more sense that a homogeneous population was being evolved than the entire human race coming from one extremely narrow bottleneck. What am I missing?

Alright alright. I get it. Didn’t have my thinking cap on. Too used to thinking diploid.

W. H. Heydt said:

Scott F said: Even if all that were “true” in some metaphorical sense, it only helps understand the “Y Adam”. It doesn’t help as much with the “mtDNA Eve”. Unlike the rest of the genes (including the “Y”), the mitochondrial “clump” of DNA doesn’t “mix”. Wouldn’t the least-common-ancestor of the mitochondria be the first eukaryote to swallow the first proteobacteria? Isn’t that the point where that particular “thread” started? If the other females at the time contributed any genetic material to today’s population, they must also have contributed their particular version of the mitochondria. Mustn’t they?

IANAB… I think of it this way…

You have a population of many females. Each will pass her unique version of mtDNA to her children. Allowing for mutations, her female children will pass their versions all to their children.

Not all females will have children, and of those that do, not all will have female children. Over time, any unique lineage of mtDNA can go extinct. Eventually, you will get a branching tree structure of related patterns of mtDNA traceable back to a single ancestral form. The earliest ancestress of the remaining traceable form becomes the “mtDNA Eve”. As various modern lineages of mtDNA go extinct, the “mtDNA Eve” will change.

Some one with good biological chops will be able to tell if I’ve got the concept down reasonably correctly for a layman.

(Maybe Part #2 will cover this, but I have to respond here first.)

I understand the part about the branching tree structure, and various “modern” lineages of mtDNA going extinct. But we have declared we’ve found the LCA of *all* “current” lineages. There is no other. Sure, other more recent lineages might go extinct, but once the progeny of the LCA have replaced all others, the LCA no longer changes. Right? Or am I missing something again?

Let me read Part #2.

Scott F said:

(Maybe Part #2 will cover this, but I have to respond here first.)

I understand the part about the branching tree structure, and various “modern” lineages of mtDNA going extinct. But we have declared we’ve found the LCA of *all* “current” lineages. There is no other. Sure, other more recent lineages might go extinct, but once the progeny of the LCA have replaced all others, the LCA no longer changes. Right? Or am I missing something again?

Let me read Part #2.

I hope you won’t mind me interfering.

Assume we see features that are denoted using letters in the alphabet. Many of the letters are in use in forming combinations such as ABCHKT and ABCLMT. Assume further that ABC is part of any combination we can find. Thus, it defines a common property shared by everyone now living. The last common ancestor is then defined as …

Well, how is the LCA defined ? It can’t be the first occurrence of ABC in the combination. Or can it ? Could LCA be an individual from the first era that everyone had this part in their combinations ?

I suddenly realise that I don’t understand what this topic is all about.

Anyway, assume the feature C is somehow mutated. Then the common part would be AB only. Surely, I presume, the LCA would be different (and maybe was living a longer time ago than the LCA for the ABC).

We can also think (in mathematical speculations) that a different part of the combinations, let’s say ABE, would become the part that is shared by everyone. Again, the LCA would change. The LCA for ABE is different from the LCAs for ABC and AB. It might be the most recent of them all, but not necessarily. It depends also on the definition of the LCA.

I admit that I am confused. A little bit of help would be appreciated.

M. Wilson Sayres Wrote:

There were several other genetic females living at the time of the person who carried the mtDNA ancestor of us all, and several other genetic males living at the same time as the genetic male who carried the Y chromosome ancestor of modern genetic males.

Apologies if this was mentioned already, but there were also many other males and females alive at the those two times who are not directly ancestral to any of us, but nevertheless related. That may seem trivial to us, but most people rarely give it 5 minutes’ thought. Genesis literalists are far from the only ones confused. I remember my own confusion; when I first heard of mtEve in the 80s I thought they had found a fossil.

Eric Finn said: I understand the part about the branching tree structure, and various “modern” lineages of mtDNA going extinct. But we have declared we’ve found the LCA of *all* “current” lineages. There is no other. Sure, other more recent lineages might go extinct, but once the progeny of the LCA have replaced all others, the LCA no longer changes. Right? Or am I missing something again?

Once again, IANAB…

As I read it, if a mondern mtDNA lineage went extinct, it would, if anything bring the LCA *forward* in time. Think about it this way for a moment… If all but one modern lineage were suddenly wiped out, the LCA for single remaining lineage would be where that lineage branched from the then-existing lineages that are now gone, which would have to be more recently than the prior LCA when other lineages still existed.

I hope you won’t mind me interfering.

Assume we see features that are denoted using letters in the alphabet. Many of the letters are in use in forming combinations such as ABCHKT and ABCLMT. Assume further that ABC is part of any combination we can find. Thus, it defines a common property shared by everyone now living. The last common ancestor is then defined as …

Well, how is the LCA defined ? It can’t be the first occurrence of ABC in the combination. Or can it ? Could LCA be an individual from the first era that everyone had this part in their combinations ?

I suddenly realise that I don’t understand what this topic is all about.

Anyway, assume the feature C is somehow mutated. Then the common part would be AB only. Surely, I presume, the LCA would be different (and maybe was living a longer time ago than the LCA for the ABC).

We can also think (in mathematical speculations) that a different part of the combinations, let’s say ABE, would become the part that is shared by everyone. Again, the LCA would change. The LCA for ABE is different from the LCAs for ABC and AB. It might be the most recent of them all, but not necessarily. It depends also on the definition of the LCA.

I admit that I am confused. A little bit of help would be appreciated.

If one goes from an LCA with an “ABC” sequence to an LCA with an “AB” sequence, the “new” LCA would have be further back in time. That is, when was the last time that those sequences–for all existing modern lineages–were connected on the pruned, branching descent tree?

Attenion: Biologist on aisle 3, please…

Scott F said: (Maybe Part #2 will cover this, but I have to respond here first.)

I understand the part about the branching tree structure, and various “modern” lineages of mtDNA going extinct. But we have declared we’ve found the LCA of *all* “current” lineages. There is no other. Sure, other more recent lineages might go extinct, but once the progeny of the LCA have replaced all others, the LCA no longer changes. Right? Or am I missing something again?

Let me read Part #2.

If the LCA had 2 daughters, but later all the mtDNA descendants of one of them die out*, then the other daughter of the previous LCA becomes the current LCA.

*Of course, that daughter might still have descendants that have at least one male somewhere in the lineage, but that’s irrelevant here.

W. H. Heydt said: If one goes from an LCA with an “ABC” sequence to an LCA with an “AB” sequence, the “new” LCA would have be further back in time. That is, when was the last time that those sequences–for all existing modern lineages–were connected on the pruned, branching descent tree?

Attenion: Biologist on aisle 3, please…

Maybe biologists have difficulty in answering questions about “ABC”-sequences, because they don’t know what type of information is being requested by those “IANAB”-persons.

I will try to reformulate the question. First, I will change the terminology and talk about MRCA (Most Recent Common Ancestor) instead of LCA (Last Common Ancestor). I feel MRCA is the better name of the two, although the meaning is the same.

If we knew all the details of the descent over millennia, we would be able to construct trees starting from a single individual (or a couple) and check if any branch of that tree extends up to the present time. Similarly, we can start from the present time tips of the branches and work our way deeper in time until our search ends up in a single node. (A single node must exist, since all life is connected. A single origin is not an assumption; it is a conclusion based on observations). This is the way MRCA is defined, if I have understood it correctly.

The same procedure can be repeated for a part of the genome (by selecting the modern tips of the branhes), provided we had detailed knowledge of the genomes of all individuals. We can use mtDNA, Y chromosome, hemoglobin or any part we wish. Each part would yield a different result.

We do not have detailed knowledge either of the decent, or of the individual genomes. We can only study the modern genomes in order to deduce information and estimate what has happened in the past.

The question is: How was the knowledge about modern genomes used to estimate the time to the most recent ancestor?

This is rather a technical question instead of a conceptual one. I am aware that the time scale was calibrated based on other information, such as the time of human settlement in the Americas.

Eric Finn said:

The question is: How was the knowledge about modern genomes used to estimate the time to the most recent ancestor?

I plan to cover this in a future post (they are coming, but there will probably only be one this coming week, y’know, with my day job and all).

A quick response for now. From the Poznik paper (and hopefully someone will correct me if I’ve misunderstood:

TMRCA = (Average number of differences observed in the genomic region of interest across all individuals reconstructed ancestor)/(Mutation rate for genomic region of interest)

The units:

Years = Mutations/(Mutations/Year)

Is this what you were looking for?

M. Wilson Sayres said:

Matt Young said:

It seems to me that Y-chromosomal Adam is not Adam at all but Noah. Noah is the last common ancestor of all living males (according to the myth), not Adam.

Matt, I’m confused. Why try to explain it in Biblical terms at all?

I can see a couple reasons to use Matt’s Noah analogy. First, it helps readers* understand that “common ancesters” doesn’t necessarily imply “first humans.” Noah had human parents, grandpaerents etc. So did Y Adam. Second, it helps readers understand that “common ancestors” doesn’t mean “sole origin of human genetic materials.” Noah’s grandchildren inherited genes from people who were not direct descendents of Noah. The same is true of Y Adam - his grandkids owe some of their genes to people outside of the Noah line. These other people weren’t the last common ancestor, but they are ancestors.

*I’m assuming readers that are fairly familiar with the biblical story and who may have already made some erroneous assumptions, based on science’s use of terms like ‘genetic Adam.’ I’d agree that making the Noah analogy makes not sense whatsoever, if your reader isn’t burdened by Judeo-Christian cultural baggage to begin with.

M. Wilson Sayres said:

I plan to cover this in a future post (they are coming, but there will probably only be one this coming week, y’know, with my day job and all).

A quick response for now. From the Poznik paper (and hopefully someone will correct me if I’ve misunderstood:

TMRCA = (Average number of differences observed in the genomic region of interest across all individuals reconstructed ancestor)/(Mutation rate for genomic region of interest)

The units:

Years = Mutations/(Mutations/Year)

Is this what you were looking for?

Thank you for your reply !

First, I do not have access to the full paper by Poznik et al., I can access only the abstract.

If the time T(MRCA) to the most recent common ancestor is estimated based on the average number of differences in the genomic region of interest, then I was definitively wrong in thinking that the similarities could somehow define the common ancestor. The ”ABC” sequence, assumed to be shared by everyone in my earlier example, would be almost meaningless in this approach.

I will be perfectly happy to wait for your future posts. Please, take your time.

Maybe you could comment in your future posts also the number of individuals in this study. Sequencing the genomes of 69 males does seem a little bit low in statistics.

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