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I was a molecular biology major a while ago, but I never think I really understood cladistics TBH. Now reading about paraphyly, it shows this:

enter image description here

enter image description here

In this phylogenetic tree [second image], the green group is paraphyletic; it is composed of a common ancestor (the lowest green vertical stem) and some of its descendants, but it excludes the blue group (a monophyletic group) which diverged from the green group.

Looking at the "simiiformes", I can understand why you would call that "monophyly", because everything is connected to a common ancestor. But why not just make the blue area a full blue triangle to make the prosimii and simiiformes one triangle/group? In the end, we all share the same ancestor, so I don't see why they are disconnected.

TBH I'm not sure how to read this at all, and am not following the Wiki description. Can you explain how the 3 terms work for a child or layperson with a better concrete example?

We are all composed of atoms, so we are all made of matter. Matter is made of particles, so we are all made of particles. But light is a particle and we are not made of light, even though in some way "we share the same common ancestor" of the quantum field. But light is still called a particle, so the triangle is the group of all particles. I'm not sure I'm getting on the right track.

A paraphyletic group is a monophyletic group from which one or more subsidiary clades (monophyletic groups) are excluded to form a separate group.

Why would they do that?

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    $\begingroup$ I don't think any child or layman will ask for an explanation of "paraphyly" ;) $\endgroup$ Feb 18, 2023 at 7:12
  • $\begingroup$ "We call all of these 'trees', but actually they are a wide range of unrelated plants." $\endgroup$ Feb 19, 2023 at 2:20
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    $\begingroup$ @KevinKostlan - your layman's explanation is more charitable than mine, which is "Taxonomy is a giant sham, genus/species etc is a description that, as we dive into the genetics, is harder and harder to force into reality. So we keep screwing with the data to try and make it fit, because "new species" is a concept the public think is cool, whereas "genetically distinct group" is not. Yes, it's messy. Blame the swedish pedant working before genes were discovered for it." $\endgroup$
    – lupe
    Feb 20, 2023 at 8:56
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    $\begingroup$ Or, less ranty - "In this case, the genetic data tells us there three distinct groups in Prosimii. However, because they all have similar features, we'd like to lump them together for identification and historic reasons. It's clear they don't particularly fit, and in the case of Lorises and Tarsiers, their grouping is in no way more closely related than Lorises and Lemurs, but this is how we can get things to fit with the existing taxonomy classification $\endgroup$
    – lupe
    Feb 20, 2023 at 9:05
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    $\begingroup$ @Lupe: "Taxonomy is a giant sham". Does it matter whether we consider a Texas cougar the same species as a Florida panther (or that there is admixture)? I think it's more important for the public to realize that "invertebrates", "trees", etc are meaningless groupings, while "bird", "bony fish" (with very few exceptions), "insects", "mollusks", "flowering plants", etc are meaningful. Still other words are half-truths: "reptile" excludes birds, but "reptiles+birds" is a clade. $\endgroup$ Feb 21, 2023 at 5:39

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These are terms to describe names we give things that don't really follow phylogeny accurately. Fish, for example - a monophyletic group involving fish would include humans, too, yet there are many cases where it's useful to talk about fish without meaning every land vertebrate, too.

From the page you link to:

The term was coined by Willi Hennig to apply to well-known taxa like Reptilia (reptiles) which, as commonly named and traditionally defined, is paraphyletic with respect to mammals and birds. Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor, including all extant reptiles as well as the extinct synapsids, except for mammals and birds. Other commonly recognized paraphyletic groups include fish, monkeys, and lizards.

If you want to use any of these labels: fish, monkeys, lizards, reptiles, it's useful to have a term to describe how those labels relate to phylogeny, hence the term paraphyletic.

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  • $\begingroup$ The quote seems a bit circular: "paraphyletic was coined to describe taxa which are paraphyletic"? $\endgroup$
    – terdon
    Feb 19, 2023 at 11:24
  • $\begingroup$ @terdon I'd paraphrase instead as "paraphyletic was coined to describe taxonomical words already in use". For reptiles, the quote also points out which specific taxa make "reptile" paraphyletic: mammals and birds, which is extra information and not circular. $\endgroup$
    – Bryan Krause
    Feb 19, 2023 at 15:42
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One very simple example that most people are familiar with is the vernacular use of "animal". Most people recognize that humans are animals and more closely related to other animals than plants. However, usually when people say "animal" in everyday speech, they mean what would technically be called "non-human animals". "Non-human animals" are a paraphyletic group, including the last common ancestor of animals and all their descendants, but excluding humans.

While fish and reptiles are good examples, due to strange tendencies of popular culture, I think that laypeople are more familiar with birds being descended from dinosaurs than mammals being descended from fish. So you could say:

Since all birds are descended from dinosaurs, you could rightfully call birds "dinosaurs", and sometimes scientists do. However, when a five-year-old says "dinosaur", they aren't typically thinking about birds but referring to a paraphyletic group: extinct scaly creatures, maybe with some feathers, but excluding modern birds. Scientists sometimes say "non-avian dinosaurs" to make this explicit.

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I put some comments further up, but if I was teaching this, my first attempt would be to "acknowledge the absurdity" - basically, that these groups clearly don't, according to the genetics, fit together.

The next bit is to talk about physical similarities - what features do the creatures share that might make someone group them together?

Then I think we'd talk about how we have two different classifications we're trying to reconcile - traditional taxonomy, which is how the entire body of research we have before genetics is organised, and modern phylogenetics.

Taxonomy groups creatures by physical features, and is broadly qualitative. It is produced by the determination of taxonomists.

Phylogenetics groups by nearest common ancestor, and is based on hard genetic data. However, it tends to ignore large physical features.

Polyphyly is just an area where two groups identified by taxonomy as closely related, share less common ancestry than a group that was not included by taxonomy - it's a taxonomic screwup, but one we can't simply fix. In time, as taxonomy is revised to take into account genetics, it is likely to be resolved, but that takes an extremely long time.

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To answer your specific questions

But why not just make the blue area a full blue triangle to make the prosimii and simiiformes one triangle/group? In the end, we all share the same ancestor, so I don't see why they are disconnected.

They are one group, called primates.

That is not an image of all the clades for those organisms, it is just an example of the types of groups. Clades can be nested. The link below may help you. Cladistics is a organization of ancestor not just arbitrary categories. A clade is literally often defined as Organism X plus Organism Y, their Most Recent Common Ancestor, and all of its descendants.

Also names for groups have history including decades of published papers refering to them. you can't just change what a name is referring too every time we learn something new. Prosimii may have been thought to be monophyletic at one time, relationships change as we learn more about them. Or it could have been named for the things in one group but not in another, because that was something useful to talk about, like lawless fish. groups have history, a paraphyletic group might all be extinct making relation ships difficult to establish or not important for the characteristic being discussed.

enter image description here

https://evolution.berkeley.edu/evolution-101/the-history-of-life-looking-at-the-patterns/understanding-phylogenies/

Using anything that does not reproduce as an analogy has a big problem, for instance changing what is or is not a planet does not make a prediction about what the origin of all those planets/not-planets are. Cladistics is a map of ancestry and evolutionary history. A paraphyletic group might still be useful if everything in the group is extinct or lives on a different continent, or share similar features. Consider the terms non-human primate, non-avian dinosaur, or non-tetrapod fish, those are groups that are paraphyletic, but still useful groupings to make for discussion. They are abasically ALL X that do not have feature Z.

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I would use reptiles as an explanation. Most people think they "know" reptiles (though they may mistakenly exclude turtles). So tell your layperson that birds are actually reptiles. If you exclude birds, it is just like having some cousins who look very different, so you decide they are not a part of your family! But that would obviously be false. In the same sense, the group 'reptile' is false, since it excludes birds. We call such false groups 'paraphyletic' because it sounds more academic than the phrase 'false group'.

It turns out there are many, many false groups as people were putting living things into categories for centuries before we had readily available DNA sequences.

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