I would agree with @glipsnort, and have stated the same.
To amplify slightly on my original comment. . . By using a folded allele spectrum, one throws away the information specifically about the oldest portion of the history of the population.
I quick glance through the paper doesn’t tell me their reasoning for using the folded AFS. Did they want to avoid using an outgroup (perhaps for philosophical reasons) to infer derived and ancestral alleles?
Dunno – I’d rather not speculate about motive. You don’t have to accept common descent, though, to calculate the allele frequency spectrum based the outgroup allele. And if that spectrum poses a stringent challenge to your model, you have an obligation to calculate it.
Not that bad of a summary.
This whole thing is ridiculous. A single couple bottleneck, how ridiculous is that.
I don’t understand why it is important either, but there is value in being honest about what the evidence does and does not show. Science at its best takes questions seriously.
Science couldn’t care less about such nonsense. Science is now making amazing discoveries with more and more a-DNA. I can wait to see the results coming out of David Reich’s lab. A lot of surprises ahead that will make the Genesis story more and more of an ancient fairy tale.
He may be characterizing Ann Gauger and Ola Hossjet (sp?) 's use of parsimony, but he did it very fiercely, so I’m assuming it’s his view about parsimony.
I was wrong: It’s spelled Hössjer. (The final “t” was a typo on my part).
Now that I’ve read the paper more thoroughly, I find I was focusing on the wrong thing. Their conclusion based on their simulations is that a single-couple bottleneck 500,000 years is consistent with the observed allele frequency spectrum. I think they’re more or less right about that. My conclusion from playing around with simulations was that 500 kya is about as far back as the AFS can take you. It’s also consistent with @swamidass’s study of the ARGweaver results. I think that they’d find that even 500 kya doesn’t give a great fit if you look at the unfolded rather than the folded spectrum, but they’re in the right ball park.
The only problem really is the last sentence quoted above, in which they suggest that minor modifications could make their model consistent with a 100 kya date for an initial couple. The paper provides no evidence whatever that this is true. It’s akin to saying, “I’ve shown that I can run 400 meters in 60 seconds. With minor modifications to my stride, I suggest that I could run that distance in 12 seconds.”
I agree. That is a pretty big leap. It’s worth pointing out to @Agauger, and I will.
I’m a bit lost at sea here, not having any formal training in the field. My inclination is to think that the single couple hypothesis is not in fact more parsimonious than a larger population hypothesis. The population scenario seems more parsimonious to my unprofessional eye because of the overwhelming preponderance of large population dynamics in observed population genetics vs. single couple events.
Also factoring in would be the recent, significant gene transfer between Sapiens, Neanderthals, and Denisovans, who trace back to a common ancestor circa 700kya.
Finally, there is the theological pointlessness of the exercise. Clearly the paper’s authors are motivated by belief in a tradition that regards Adam and Eve as the genetic ancestors of all living humans. But the Adam and Eve of tradition were talking with God and practicing agriculture. Could an Adam and Eve like that have existed 500kya? Archaeologists and anthropologists have strong evidence that higher order language is no older than 200kya, and agriculture no more than about 15kya, IIRC. So the whole exercise seems futile to me.
But I am no expert, and I’m learning a lot by just following this conversation. My view of parsimony with regard to biology is that the forces that prevail in our world today are the most likely explanations of what prevailed in the past. Therefore, what is barely possible mathematically is not the definition of parsimony, even if it makes the math a little easier to solve. I invite you to disabuse me in exquisite detail of any n00b notions that I have expressed so that I can keep learning!
@Chris_Falter, parsimony is poorly defined in many contexts, perhaps like this, and it is a generally bad way of modeling data in cases where reality is complex and data is limited. Such as in this specific question.
I would describe what you’re talking about not in terms of parsimony, but in terms of the prior probability you’re assigning to different possibilities. (An assignment I think is reasonable – but someone with a strong belief in the literal truth of Genesis might assign a different prior.)
Agree with glipsnort that Bayesian priors are not the same as parsimony.
In general people say that when all else is equal one should choose the most parsimonious hypothesis. As soon as you consider a case where A is most parsimonious, but there is a little bit more evidence in favor of B than in favor of A, you can see the lack of clarity in all this. Exactly how much evidence does it take to override parsimony and conclude in favor of B? Chris Falter made it sound as if one requires a vast amount of evidence in favor of B to do that. But when people say “when all else is equal” they are implying that any tiny amount is enough to invalidate the use of parsimony.
I’m leaving aside the use of “parsimony” as a justification for minimum-steps methods for inferring phylogenies. There the declaration that the count of number of changes is a numerical definition of parsimony is, to my mind, arbitrary. It is a whole different discussion, which I spent years working on. Don’t get me started on that …
After this article: A First Couple? Here’s the Backstory | Evolution News. Here is another article from @Agauger responding to us here.
Why did most think a bottleneck of two was impossible? I can’t say for sure, but at least in Dennis Venema’s case it seemed to be his confidence in the many reported effective population sizes of 10,000. What he missed was the fact that averaging over millions of years would mask a sudden sharp bottle neckdown to two individuals if recovery is rapid.
She is absolutely right here.
Now over at Peaceful Science they are discussing this paper. I am pleased to see it. And I can even answer a few questions right away, such as why we didn’t use a more powerful tool such as ARGweaver .
The answer is simple: built-in evolutionary assumptions. We tried to keep our math as free as possible from assumptions about evolutionary history.
Well that is an odd objection. Argweaver doesn’t have a built in assumption like this.
That is also why we didn’t use the derived frequency spectrum, which would have entailed comparing chimp and human sequences to determine which human allele was likely to be ancestral and which mutant (using the chimp as the outgroup). If no evolutionary relationship is there, what is the point in using chimps as an outgroup? It is permitted, in any case, to use a folded allele frequency spectrum in cases where no appropriate outgroup exists.
@glipsnort, this explains why they did not use the derived frequency spectrum. It looks like they are really going for a de novo creation model here. Unlike the GAE, however, in this case, they do fall prey to the “appearance of common decent” problem. Why did God create AE such that it appears we share common ancestry with the great apes?
There are multiple directions we could go. We may use something like ARGweaver in future papers, but we would want to compare its results with what we have now. We could test the effect of population structures, migration, and subdivision on effective population size and the time required to match current genetic diversity.
I am all for this. I’m just not sure what they gained from this study in the first place.
For Joshua Swamidass: Actually, we mentioned HLA, which is home to many examples of putative trans-species polymorphisms. This an area I would like to take up because I think it is the way forward and may provide some answers to our origin that other regions of the genome can’t. More later.
Yes, I do think this is where things well get interesting.
As for ghost lineages, as far as I can tell they will shift things further in the past. No problem. Remember, I’m OK with 2 million years!
Yup, I think @Agauger’s willingness to go that far back really makes her position safe from falsification by everything but, possibly, trans-species variation.
@Joe_Felsenstein, she includes a discussion of Parsimony too. I think she wasn’t investing that word with much weight.
Well, as you point out, it’s not safe from falsification by any gene you care to name, since they all show that humans are related to other apes. A bottleneck of 2 (or perhaps a dozen or so, given those cross-species polymorphisms) may not be falsifiable, but de novo creation of genetic A&E certainly is, absent the auxiliary hypothesis of a deceptive deity.
Well yes. That “safe from falsification” was in a particular context.
I do think that the issue of “appearance of common descent” is not necessarily a deal breaker, but it raises serious theological questions. Those questions have to be articulated and engaged in a sensible way for them to make their case. As far as I can tell, they do not do this here, or elsewhere.