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.