At what point does a clade become a certain taxonomic rank?

[u/DeltaWaffle_]

As per title

Like, what makes a clade a phylum instead of a domain, or class? When does a genus become a separate family from the original? Would it be like “domain is what type of cell it is at the most basal of all, bacteria and archaea differ so much at a basal level where as none of eukaryota doesn’t differ enough to be different domains. Kingdoms are something something. Phyla are the basal bodyplans of their kingdom, and class is how that bodyplan is specialized” or is that an oversimplification?

[u/stillinthesimulation]

At the end of the day, taxonomic ranks are artificial constructs created by humans to organize a complex spectrum of life. There are no hard lines in nature but our minds demand them. The contradiction is inevitable. These categories can be useful but there is no inherent truth to them. Organizing mammal groups can make sense and organizing groups of fungi can as well, but don’t look for any clear rules to compare what makes a family of mammals vs an order of fungi or vice versa.

[u/DeltaWaffle_ → u/stillinthesimulation]

I understand that, but at where is the point between each rank? When doing taxonomy, when do you classify a clade as a kingdom, and when do you classify it as a phylum? It can’t be entirely arbitrary because the whole system was created to bring order to the chaos that is evolution, so what do people used to define the ranks?

[u/stillinthesimulation → u/DeltaWaffle_]

The ranking systems were created before we knew what genes were. Kingdoms and phylums were locked in a long time ago. Once we started sequencing genomes we realized it was a lot messier than we thought. I was taught there were five kingdoms when I was a kid. Some biologists now argue there are actually over 30. Others say there could be hundreds more at a micro level we can’t really fathom. It’s still a largely useful system of categorizing life so long as you accept it’s just an approximation of reality.

[u/throwitaway488 → u/stillinthesimulation]

"30 Kingdoms" this is just lumper/splitter fights unless there is a strong definition for what defines the concept of a kingdom.

[u/stillinthesimulation → u/throwitaway488]

We used to put protists as a kingdom but we now know that amoebas are closer relatives of you and I than they are to parameciums. Eukaryotes alone are far more diverse and difficult to lump together than we once thought. But on the prokaryotic side it becomes way more challenging. It’s why I’m saying the concept of a Kingdom is useful in some circumstances, but isn’t a universal reality across life. Biology just isn’t that clean.

[u/DeltaWaffle_ → u/stillinthesimulation]

Yes I understand that, what did the people back then use as a basis for their domains, kingdoms, and phyla, that’s really my main question. You see I’m doing a hard spec-evo project, and I want to know how when doing the archaic way (because I start all my projects in the mind that you divide the cladeogram taxonomically until the phyla, and from there you evolve naturally using the modern model)

[u/Xrmy → u/DeltaWaffle_]

It's literally "I made it up"

[u/Jake_The_Great44 → u/DeltaWaffle_]

I know its really unsatisfying, but there are no criteria for any rank other than species.

We use terms like kingdom Animalia and kingdom Plantae because animals and plants are both very broad groups that also look very different, so they look like two distinct groups. The language I'm using is very vague because how broad a group has to be to be a kingdom is arbitrary.

Birds look like a distinct froup from reptiles, which is why class Aves and class Reptilia are separate, but we now know that birds are descendants of reptiles and are more closely related to crocodiles than crocodiles are to lizarsds, so these ranks very often don't reflect evolutionary histories.

Phyla (at least in animals) are roughly defined by distinct "body plans" but how different two taxa need to be in their "body plans" is not defined.

If you want your speculative evolution project to have taxonomic ranks that somewhat resemble Linnaean ranks, you are going to have to get a feeling for what kingdoms, phyla, classes, etc. generally consist of. If you can come up with a handful of very broad divisions, you would qould probably call those kingdoms, and then you would choose some groups within those to call phyla, and so on.

[u/lpetrich → u/Jake_The_Great44]

Some taxonomy jargon about taxa:

• Monophyletic: a taxon includes an ancestor and all of its descendants, and no others.
• Polyphyletic: the overall ancestor (if any) is not in the taxon, like Haemothermia, warm-blooded animals.
• Paraphyletic: a taxon includes an ancestor, only some of its descendants, and no others, like Pisces, fishes, and traditional Reptilia, reptiles.

Cladistics only recognizes monophyletic taxa, while traditional taxonomies often include paraphyletic taxa and sometimes also polyphyletic ones. But some non-cladistic taxa are still used as convenience taxa, like all three of my examples.

• Haemothermia = Aves + Mammalia (likely supertaxa of these two and maybe others, but still at least two)
• Pisces = Vertebrata - Tetrapoda
• Traditional Reptilia = Amniota - Aves - Mammalia (Reptilia is nowadays shrunk and made monophyletic)

I sometimes see names of non-cladistic taxa put in scare quotes: "Haemothermia", "Pisces", "Reptilia".

[u/Jake_The_Great44 → u/lpetrich]

Reptilia is nowadays shrunk and made monophyletic

In my experience it's a lot more common to synonymise Reptilia with Sauropsida, which is the reptile total group (everything more closely related to extant reptiles than to mammals), which makes it broader than the traditional Linnaean Reptilia and also means it includes birds.

[u/Levangeline → u/DeltaWaffle_]

It was mostly morphology. Sometimes behaviour/ecological niche for animals and plants, and chemical profiles for fungi and plants.

Falcons for example. Morphologically they resemble hawks and eagles. They're also agile aerial predators, so they were classified as close relatives.

Turns out, they're actually more closely related to parrots. There are morphological hints to this (Falcons and parrots both moult in a weird way and have similar beak mechanics), but we didn't really piece that together until it was backed up with genetic evidence, because the relation to hawk and eagles just seemed so obvious.

Plants are especially notorious for looking extremely similar to each other even if they're completely unrelated, or looking extremely different from their close relatives.

But yeah, for most of taxonomic history, we were classifying stuff based on how it looked.

[u/Acachupawah → u/DeltaWaffle_]

Por qué le dan downvote a esto, es súperinteresante su proyecto y su pregunta. Dejen de molestar

[u/In_the_year_3535 → u/DeltaWaffle_]

Morphological classification follows the tradition of Linnaeus and hip-shots based on pronounced traits in aggregation. Computational phylogenetics uses statistics in a similar vein because at the end of the day it's all very subjective. Reconciling the two approaches is most common today and all effort is made to not make delineation arbitrary.

[u/DeltaWaffle_ → u/In_the_year_3535]

Ok, tell me more of the morphological approach, at what point do each rank become different from each other? Specifically from domain to phyla

[u/Bdellovibrion → u/DeltaWaffle_]

If you want a quick and very imprecise answer:

Domain is based in fundamental differences in cellular organization at a microscopic level (does it have organelles etc?).

Five-kingdom paradigm was based on nutrition type (auto- vs hetero- vs saprotroph) and cell count (multicellular vs unicellular).

Phylum was based on general body plan and notable macroscopic features (among other things).

For a given organism, they'd start with the high level ranks first and continue with a top-down classification algorithm.

[u/DeltaWaffle_ → u/Bdellovibrion]

Thank you! This is exactly what I was looking for!

[u/Bdellovibrion → u/DeltaWaffle_]

Cheers!

[u/DeltaWaffle_ → u/Bdellovibrion]

Happy cake day by the by!

[u/In_the_year_3535 → u/DeltaWaffle_]

Domain and phylum aren't even original taxon, kingdom and class were originally the largest; phylum is 19th century and domain is post advent of DNA sequencing. Originally, there were three kingdoms (plant, animal, and protist) that fit in with the classical notion of how life looks and moves. Understanding taxonomy is understanding its history and the Wikipedia pages for the divisions (domain, kingdom, etc.) do I better job than I can.

[u/EebstertheGreat → u/In_the_year_3535]

The Linnaean kingdoms (regna) were actually Animale, Vegetabile, and Lapideum, i.e. animal, plant, and mineral, often called today "animal, mineral, or vegetable." And microorganisms were considered to be either animals (protozoa) or plants (protophyta, and later Monera). Protista (which included Monera) was introduced by Ernst Haeckel.

The only ranks Linnaeus used were regnum, classis, ordo, genus, and species. The ranks of domain, phylum/division, legion, cohort, family, and tribe were added later, as were many that are no longer in widespread use (e.g. empire, dominion, alliance) and numerous intermediate ranks (e.g. subclass, superorder). And in botany, the ranks of section, series, variety and form.

[u/In_the_year_3535 → u/EebstertheGreat]

Indeed, it appears what I could do was a low bar.

[u/Romboteryx]

Ranks are just a useful leftover from classic Linnean taxonomy that we retrofitted clades onto. We simply use them for convenience as a sort of landmark along the long march of clades.

As for how clades are fitted onto ranks, often people just look for the most encompassing clades that fit the original pre-cladistic definition. For example Sauropsida is the clade that comes closest to encompass all the animals traditionally placed in the class Reptilia, so the two terms are used interchangeably.

[u/GoliathPrime]

I've never gotten a clear answer. At certain points the divisions seem arbitrary or in need of an update. I think genetics is the determining factor today, but a lot of important literature still uses the old pre-genetic morphology-based system. It's the partial integration between the genome project and linnaean taxonomy that's causing the problems. It takes a considerable amount of work to update centuries of established classification, but until everything is switched over to the genetic class system, no clear answers are possible.

[u/EebstertheGreat → u/GoliathPrime]

There is also not a universal consensus that taxonomists ought to prioritize cladistics. There is a strong consensus, but there are still holdouts who push for a system based on synapomorphies or even other morphological systems. For instance, the late Cavalier-Smith was extremely influential, and his taxonomy was intentionally not strictly cladistic. For instance, he listed Protozoa as a paraphyletic kingdom, treating it sort of like an evolutionary grade (though that's not a perfect description either).

[u/Impressive-Target699]

It's all fairly arbitrary. A "family" of mammals doesn't necessarily equal a "family" of plants or fish. That's partly due to biology of the organisms themselves--plants are very different from animals, so it can be harder to determine even where to draw the "species" line--but mostly due to the fact that mammal researchers apply their own criteria to mammals, plant researchers apply their own criteria to plants, fish researchers apply their own criteria to fish, etc.

[u/tpawap]

Maybe you're looking at it the wrong way around. You start with all the (extant!) species, and then group all that are "very similar" into families. Then you take the families and group those that are still "somewhat similar" into genera. Repeat until you reach the "everything" box.

[u/DeltaWaffle_ → u/tpawap]

The thing is I haven’t actually done the whole process of evolving my species yet (this question is for a hard spec-evo project I’m picking up again btw) so there are no species for me to reverse create the taxonomy with, only a simple cladeogram of the body plans I want used for what I guess would be the kingdoms of the project (radiazoa, and xenobilatariazoa currently are the only two I have the body plans mapped out yet, which are radially and bilaterally symmetrical animals respectively. I’m still working on a name the plant kingdom, and any other multicellular kingdoms that are worth exploring that isn’t just sessile and motile animals, plants, and fungi, seeing how radiazoa covers 3 of the four basis rn) basis for all my evolutionary shenanigans

[u/Relevant-Cup5986]

there is no prcise point, ranks are artificial constructs that correspond to what looks different to the people making them.