Talk:Incomplete lineage sorting

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Fig. 2

(Moved from User talk:Peter coxhead.)

Is the fig 2 really a incomplete lineage sorting? I think it should be a HGT, right?

It doesn't fit the definition. It is not a random retention of ancestral genetic polymorphisms in descendant species. ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 08:50, 3 November 2022 (UTC)[reply]

@Interaccoonale: Fig. 2 illustrates a situation which is not hemiplasy/incomplete lineage sorting, but only appears to be, as the text says: "This is illustrated in Figure 2. ... Studying only the final states of G in the three species makes it appear that A and B are sisters rather than B and C, as in Figure 1, but in Figure 2 this is not caused by hemiplasy." I've edited the caption to try to make this even clearer. Peter coxhead (talk) 09:03, 3 November 2022 (UTC)[reply]

Thanks, I get it.

I misunderstood that you meant hemiplasy is just one type of ILS, and the example 2 is a non-hemiplasy type of ILS.

I think making it clear in the lead that hemiplasy is a synonym of ILS is a good idea. And replacing hemiplasy with "incomplete lineage sorting" in the "example 2". Because the word hemiplasmy is seldom used. ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 09:16, 3 November 2022 (UTC)[reply]

I think the statement "The particular kind of incomplete lineage sorting shown in Figure 1 has been called hemiplasy" should be revised. Apperently it implies that there could be non-hemiplasy kinds of ILS. ——🦝 The Interaccoonale ^{Will be the raccoon race}_{(talk・contribs)} 09:19, 3 November 2022 (UTC)[reply]

@Interaccoonale: let's go back to some definitions. This website defines ILS as "anything other than perfect segregation of all alleles into all lineages". I'll call this "ILS₁". The paper that introduced the term hemiplasy has the definition: "the topological discordance between a gene tree and a species tree attributable to lineage sorting of genetic polymorphisms that were retained across successive nodes in a species tree". So combining these definitions, hemiplasy results when ILS₁ leads to discordance between a gene tree and a species tree. Does ILS₁ always have to lead to this discordance? No. In Figure 1 in Incomplete lineage sorting, the species tree has B and C most closely related, but the gene tree suggests A and B are. Now suppose in Figure 1 the blue line didn't go to B and the red line split at the base of B and C, going to both. Is there ILS₁? Yes, because the two alleles G0 and G1 were both present in the ancestor of A, B and C, but are not both present in all the descendant lineages – they were not perfectly segregated. Is there hemiplasy? No, on the definition above, because the gene tree and the species tree now both agree that A is separated from B+C.

The problem, I think, is that ILS is used to mean hemiplasy, because ILS₁ which does not result in discrepancies between gene trees and the species tree is not interesting. So ILS is effectively defined (as it is in the first sentence of the current version) as ILS₁ that leads to hemiplasy. But in principle, they are not the same. Peter coxhead (talk) 15:51, 3 November 2022 (UTC)[reply]