What is Incomplete Lineage Sorting?

Continuing the discussion from What if Adam was just a character in an Ancient Creation Story?:

Yes, there is incomplete lineage sorting (ILS) between humans and the great apes. This means that different parts of the genome have different phylogenetic topologies.

No, this does not mean that we were never in one place long enough. Rather it merely tells us that the ancestral population 6 to 10 million years ago, was a large population, not a single couple, but who thinks it was a single couple at this point any ways?

@jongarvey @pevaquark @John_Harshman


Thanks for the clarification, though probably most who think of a single couple bottleneck don’t think any evidence of a larger population size in an ancient shared ancestry is that interesting anyways.

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Pretty much. I’m just not sure how this important in the larger conversation except for confusing people who think (or argue) evolution must produce perfect trees.

Except, we expect that when several species branch off a single lineage in a “short” amount of time, there will be ILS, which means they will not be in a perfect tree. We expect there to be conflicts with a perfect tree.

Creationists? Of course creationists can’t believe in incomplete lineage sorting, because they don’t believe in lineages, at least not within apes. Of course what ILS tells us here is that the population size divided by duration of the combined human/chimp lineage, after separating from the combined human/chimp/gorilla lineage and before separating into human and chimp lineages, was not small. It doesn’t seem to have any relevance to human origins after that split; it doesn’t preclude a bottleneck of 2 along the human lineage.


That isn’t true. ILS is a concept that can be readily demonstrated in simulations, by math, geometrically/visually, and also demonstrated in populations everyone agrees shares common ancestors. There is no reasons that creationists can’t come to understand it.

They might still say this isn’t the right explanation from ILS with humans and the great apes, but they might stop making absurd arguments like this one from Doug Axe:

Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there. Instead of a nested hierarchy of similarities, we see something more like a mosaic. According to a recent report [1], “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…” // That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question.
The Gorilla Who Broke the Tree - Biologic Institute

This is a totally indefensible line of reasoning. We expect imperfect trees in common descent, so ILS is not evidence against CD. Why then would anyone present it as evidence? The clue is in the quote. Axe is arguing against “Darwin”, who knew nothing of genetics, let alone population genetics. The poor guy is dead too, and can’t defend himself. :smile:

At some point, I hope that Axe catches up what we know about population genetics. If his other arguments against evolution are as strong as he thinks they are, he should have no need for obviously invalid arguments like this, right?

Don’t forget about the gorrilla in the room. It is a good read in itself:



This quote from Axe is pretty interesting:

Until recently, the answer was that a real family tree should generate a fully consistent pattern of similarities.

@John_Harshman, when was ILS first noted in the literature? How many decades before 2012, when Axe wrote this line?

A cursory search in google scholar and pubmed found this article from 1992 mentioning ILS by name, but the way the authors mention it so casually implies that it was by no means a new idea then.


Looking at some review articles, like this one:

they highlight papers as far back as 1965:


@swamidass, I think you prove my point. Axe refuses to believe that which is inconsistent with his prior beliefs, turning it into an argument against evolution. For the same reason, creationists who claim to accept microevolution consistently heap scorn on any examples thereof, like peppered moths and Darwin’s finches.

But I don’t think Darwin’s ignorance of genetics is relevant. Axe’s claims don’t turn on Darwin, just on a misunderstanding (refusal to understand?) of modern biology unrelated to history.

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“Old Earth Creationists” are constantly amazing… scattering their assertions in all directions!