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I am thinking about this thought experiment: Suppose we have three taxa which are grouped into the following tree: {{A,B},C}, clearly {B,C} is a paraphyletic group. But if A go extinct in the near future, we are left with {B,C} only, then can the group be called monophyletic?

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  • $\begingroup$ As long as you don't say A is OUT of the BC group, This is a monophyletic group yes. $\endgroup$ – Untitpoi Mar 11 '18 at 15:27
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To expand on Remi.b's answer, groups are defined based on all the species we know about. This includes extinct species. So in your example, the group {B,C} is paraphyletic regardless of whether A goes extinct or not.

But what if A went extinct ages ago and we don't know about it at all? In that case we would only have B and C to base a group on, and they are the only descendants of their common ancestor that we know about, so we would indeed define {B,C} as monophyletic.

The question comes when we discover A's existence, and that it is more closely related to B than to C. At that point we have a choice: expand the definition of group {B,C} to include A, in which case the group becomes {{A,B},C} and is monophyletic, or keep the group {B,C} and accept that we were wrong about it being monophyletic, it was really paraphyletic all along.

You can see these processes happen as paleontology and cladistics advance. Birds used to be classified differently from dinosaurs, but as our knowledge of how birds are descended from dinosaurs increased paleontologists chose to classify them as a subset of dinosaurs, keeping the group "dinosaurs" monophyletic.

On the other hand as our understanding of how mammals/birds are descended from reptiles and tetrapods are descended from fish increased, making both of those groups paraphyletic, the attempts to redefine them as clades have largely failed, so they are now considered paraphyletic groups. "Amniotes" has replaced "reptiles" as the name of the clade containing reptiles, mammals and birds, and "Craniata" is the monophyletic group containing various fish and tetrapods.

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To be strict about the definition, a monophyletic group is a group that contains the common ancestor and all of its descendant. This means {{A,B},C} is a monophyletic group only if you consider all of the shared ancestors until the MRCA of them all.

If A get extinct, it still remain in that {{A,B},C} (and their common ancestors) are a monophyletic group. You do not remove A from the group because it is extinct.

Of course, this means that to have a monophyletic group we should be able to name every single species (or even every single individual given how messy is the concept of species; see here) that is descendant from an ancestor but we never do that. The most important is to not willingly ignore or include a species that should not be ignored/included. Here you would ignore A under the excuse that it is extinct and that would be wrong.

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