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Post by John on Jun 22, 2010 13:21:40 GMT -5
Hey science nerds, I have a question. I imagine this could get technical. What's a clade?
From my reading of Wikipedia it appears to be a non-specific group of related organisms. So you could talk about the vertebrate clade if you were talking about all vertebrates, or the the Hominidae if you were talking about gorillas, chimps and humans.
Is that right? A clade is like a circle you draw around related critters, but you can change the "size" of that circle to include very few or very many creatures depending on what you are discussing?
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Post by shailynn on Jun 22, 2010 13:36:53 GMT -5
uhm... yeah.. that's what it means.
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Post by John on Jun 22, 2010 13:58:09 GMT -5
wow. I got an eye roll for that? Jeez...
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Post by Marky Mark on Jun 22, 2010 14:26:57 GMT -5
/incoming wall of text Clades (or "monophyletic" groups) comprise an ancestor and ALL of it's descendant lineages. They can be of any size, from all of life to a single genus of insects, as the frame of reference for a clade is always the starting ancestral lineage in question. The reason that clades are so important to evolutionary biology is that they are taxa that are based on real evolutionary history, rather than on other characteristics. The reason it's an issue is that many folks named and classified organisms prior to the foundation of Darwinian evolution. The classic example of this issue is Reptilia. If you consider Reptiles as a group without thinking about evolutionary history, most folks would exclude birds (they don't really look like reptiles, they're warm blooded, etc.). But, the prevailing evolutionary hypothesis based on the best available data is that birds branched off the tree of life from a dinosaur-like lineage: So, if someone were to talk about reptiles as an evolutionary lineage, they would have to include Aves (birds). To not do so would render Reptilia a paraphyletic group (an incomplete portion of evolutionary history that only includes an ancestor and SOME of its descendants). Another good example of this is in cockroaches. Cockroaches (Order Blattaria) and termites (Order Isoptera) were taxonomically categorized early on in entomological science. Molecular data, however, suggest that termites acutally evolved from a wood-boring, subsocial cockroach ancestor (similar to the extant genus Cryptocercus). Basically, Cryptocercus and Isoptera are sister taxa (share a most recent common ancestor). Here, all termites evolved from a common ancestor (i.e., the lineage that split from the common ancestor of Cryptocercus and termites), making this order a complete evolutionary lineage (= a clade; = monophyletic). Blattaria, on the other hand, is not a clade as initially described (it's paraphyletic). To make a monophyletic cockroach lineage, you must include termites.
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Post by Bob on Jun 22, 2010 14:31:02 GMT -5
Well said, Dr. Mark.
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Post by John on Jun 22, 2010 14:41:07 GMT -5
ok, I had to read that like six times. Helpful, but let me try and translate into dumb-guy.
So, pre darwin, a bunch of naturalists said "roit, over 'ere we 'ave Order Cockroach, and then way over 'ere we 'ave Order Termite. Very similar but obviously very different, wot wiff awl the wood eatin' and wot naught.".
Then we invented genetics and discovered they weren't so different after all. Like, a long time ago there were cockroaches, and some of them decided to live underground during the holidays. And some of those underground holiday roaches said "It's rather lovely down here, I think we'll stay." Sadly, the holiday roaches died off, leaving only the above ground cockroaches, and their subterranean brethren the termites.
Therefore, using the pre Darwin grouping of Cockroaches without including Termites is bad-wrong, BUT since it's so entrenched (ala "Birds are separate from Reptiles") we are stuck with messy taxological identification, and should really refer to the cockroach clade inclusive of termites. Basically?
Can you explain the diagram you linked? Shouldn't birds be in the blue bits if you want to make that a for-realz clade?
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Post by Bob on Jun 22, 2010 14:54:56 GMT -5
Also, by request
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Post by Marky Mark on Jun 22, 2010 15:19:49 GMT -5
ok, I had to read that like six times. Helpful, but let me try and translate into dumb-guy. So, pre darwin, a bunch of naturalists said "roit, over 'ere we 'ave Order Cockroach, and then way over 'ere we 'ave Order Termite. Very similar but obviously very different, wot wiff awl the wood eatin' and wot naught.". Then we invented genetics and discovered they weren't so different after all. Like, a long time ago there were cockroaches, and some of them decided to live underground during the holidays. And some of those underground holiday roaches said "It's rather lovely down here, I think we'll stay." Sadly, the holiday roaches died off, leaving only the above ground cockroaches, and their subterranean brethren the termites. Therefore, using the pre Darwin grouping of Cockroaches without including Termites is bad-wrong, BUT since it's so entrenched (ala "Birds are separate from Reptiles") we are stuck with messy taxological identification, and should really refer to the cockroach clade inclusive of termites. Basically? More or less, yes. Basically, a group of roaches adapted to subsocial living and eating wood by incorporating symbionts (sound termitish? ). This lineage split into two groups, the ancestors of a cockroach lineage likely bearing close similarity to this progenitor lineage ( Cryptocercus) and the lineage that would adapt further (via random mutation) to become more highly social and more efficient at using wood (termites). Termites explosively radiated due to these new adaptations, whereas poor little proto- Cryptocercus did not (it's the horseshoe crab). Sure. The point of the diagram is show that if you just think about Reptilia as things that we think of as reptiles (turtles, lizards, dinosaurs, crocs), you do not have the full evolutionary picture. What is circled is the non-evolutionarily informed picture of reptiles. The "fo'-realz" clade would be exactly what you described: Reptilia + Aves . The issue is that we used to name things without thinking about evolution (not really Linneaus' fault...it wasn't around then). After the neo-Darwininan revolution (Darwin + genetics), we started grouping things as real evolutionary units. But there's a lot of mis-mash, and we are always revising evolutionary hypotheses (more fossils, more genes, more data). Interestingly enough, there are some evolutionary biologists who want to get rid of the classical linnean nomenclature and adopt the "phylocode". Here, every species gets a number (three guesses on who would be #1...and two don't count). The reasoning behind this is that evolutionary hypotheses are always being revised with more info, so the static classifications will never be truly cladistic. I personally don't like it because of the horror of thinking about revising the whole system to numbers (I study species 13347263843...w00t!), but there is some merit to the debate.
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Post by Scott on Jun 22, 2010 15:30:42 GMT -5
No way should they get rid of Linnean Nomenclature...The Latin(faux latin?)names give things far more character.
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Post by John on Jun 22, 2010 15:52:18 GMT -5
Ok, the horseshoe crabs bit is throwing my head for a loop. The reason I even started looking into this is because I was trying to figure out what a "basal" form was, but to understand that I had to figure out what a clade was. Anway, you've got your horseshoe crab. He's got some offshoots, one of which turns into the lowly 'roach, who then spits out a buncha termites. Now, do I have this right... I can talk about the "horshoe crab clade" which contains horseshoe crabs, roaches, and termites, and I can talk about the cockroach clade, which contains roaches and termites, and I can talk about the termite clade that has a bunch of disgusting wood eating maggots. Am I following correctly? Now, a "basal" form... is the horseshoe crab the "basal" form of its roach and termite encompassing lineage? P.S. I got into this stuff because Andy is into dinosaurs now. I'm catching up on my dino knowledge and it's lead me off on this whole evolutionary tangent. BUT! Did you know we might get "Brontosaurs" back?! How exciting! On the other hand, they might have to lose "Triceratops" and call if freaking "Agathaumus". Yuck! Dinosaurs were so weird!
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Post by Marky Mark on Jun 22, 2010 16:38:47 GMT -5
Ok, the horseshoe crabs bit is throwing my head for a loop. The reason I even started looking into this is because I was trying to figure out what a "basal" form was, but to understand that I had to figure out what a clade was. Anway, you've got your horseshoe crab. He's got some offshoots, one of which turns into the lowly 'roach, who then spits out a buncha termites. Now, do I have this right... I can talk about the "horshoe crab clade" which contains horseshoe crabs, roaches, and termites, and I can talk about the cockroach clade, which contains roaches and termites, and I can talk about the termite clade that has a bunch of disgusting wood eating maggots. Am I following correctly? Now, a "basal" form... is the horseshoe crab the "basal" form of its roach and termite encompassing lineage? P.S. I got into this stuff because Andy is into dinosaurs now. I'm catching up on my dino knowledge and it's lead me off on this whole evolutionary tangent. BUT! Did you know we might get "Brontosaurs" back?! How exciting! On the other hand, they might have to lose "Triceratops" and call if freaking "Agathaumus". Yuck! Dinosaurs were so weird! "Basal groups" are lineages that split off prior to the formation of a clade long in the evolutionary past. They lack the derived characteristics shared by all members of the sister clade. A classic example of a basal lineage is in a group near and dear to my heart: the Hymenoptera: So, you have Xyeloids, which are the basal lineage. These guys lack a lot of the characters that the other Hymenoptera have (since they split off so early and were not mating with the lineages that adapted in different ways). Other groups (like Unicalcarida, Vespina, Apocrita) share more and more derived traits (keeping some older traits and accumulating adaptations, such as the bendy waist that is found only in Apocrita). So, in this example, you can talk about Hymenoptera (the basal Xyeloidea + all the other hymenopteran groups) as a clade. You can also talk about Vespina (Orussoidea + Apocrita) as a clade as they share certain traits that the more basal groups don't have. Finally, you can talk about Apocrita as a clade, as it excludes all the basal lineages who split before the bendy waist evolved. So, yes Virginia, what you said is correct: you can have three clades in your example: Horseshoe crab + roach + termites (shares traits that other things don't have), roach + termites (shares traits that horseshoe crabs don't have), and termites (has some traits that only termites have). P.S.: Dino phylogeny is a bitch. No DNA...yet . Of course, we could just say fuck it:
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Post by Bob on Jun 22, 2010 16:49:42 GMT -5
Hey, show some respect.
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Post by John on Jun 22, 2010 17:10:57 GMT -5
P.S.: Dino phylogeny is a bitch. No DNA...yet . For sure. I actually just started "The Selfish Gene", and I'm looking for a good book on the Pre-Cambrian explosion and I realized I needed to brush up on my biology. Thanks guys, this has been a huge help. This whole stuff with giving species latin names is a lot more loosey goosey than I realized. Apparently you just need to have the name you pick published in a journal and then convince everyone to use that name? Is that real? I always thought there was an international board that approved or denied latin naming. There's a big shitstorm in paleontology because some dudes described a new dinosaur and self published their work on lulu.com, and all the paleontologists are all "shit. well yeah, I guess we have to call that dinosaur the name he picked. I don't like it, but whatya gonna do?" I can really see the appeal of just assigning numbers.
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Post by Marky Mark on Jun 22, 2010 18:13:05 GMT -5
P.S.: Dino phylogeny is a bitch. No DNA...yet . For sure. I actually just started "The Selfish Gene", and I'm looking for a good book on the Pre-Cambrian explosion and I realized I needed to brush up on my biology. Thanks guys, this has been a huge help. This whole stuff with giving species latin names is a lot more loosey goosey than I realized. Apparently you just need to have the name you pick published in a journal and then convince everyone to use that name? Is that real? I always thought there was an international board that approved or denied latin naming. There's a big shitstorm in paleontology because some dudes described a new dinosaur and self published their work on lulu.com, and all the paleontologists are all "shit. well yeah, I guess we have to call that dinosaur the name he picked. I don't like it, but whatya gonna do?" I can really see the appeal of just assigning numbers. There are naming conventions and rules to govern them, but they differ a bit depending on what organismal type you work on (plants, animals, fungi, bacteria...). The problem is that many non-systematists (folks who specialize in phylogenetics and classification) try and name things without examining precedent (because they don't get the rules). I've had to deal with this a bit with the whitefly I used to work with (not quite as flashy as a new dino, but what can ya do ). Some fucktard decided to re-name it to make himself famous, but his evidence was total garbage and there was already an established name for it in the past literature (this species was lumped previously, so the new name should have reverted back to the old name as to the conventions of nomenclature). Turns out that the phylogenetic evidence didn't support a new species delineation either. BUT, people still use this fucking new name. Just goes to show that bad ideas can really stick around. I'm a bit torn about using numbers for species. Binomials aren't perfect by any stretch, but there are some pretty big logistical issues with relying solely on numbers (it'll be great for databasing, but fucking awful for people to keep straight).
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Post by Bob on Jun 22, 2010 18:19:29 GMT -5
This whole stuff with giving species latin names is a lot more loosey goosey than I realized. Apparently you just need to have the name you pick published in a journal and then convince everyone to use that name? Is that real? I always thought there was an international board that approved or denied latin naming. There's a big shitstorm in paleontology because some dudes described a new dinosaur and self published their work on lulu.com, and all the paleontologists are all "shit. well yeah, I guess we have to call that dinosaur the name he picked. I don't like it, but whatya gonna do?" Yep, that's about the whole of it. I mean, Strigiphilus garylarsoni is so-named because the taxonomer liked Gary Larson. Hella animals are named after celebrities, people's kids, etc. Self-publication is a relatively new thing in science (well, it's an extremely old thing in science, but it's new in terms of modern peer-reviewed, legitimate science scholarship). I've always been a bit fire and brimstone about it from a publisher perspective, but hardcopy print journals will be totally obsolete within a generation, and unless publishers adapt to Open Access sooner than later, you'll start seeing more and more stuff published on lulu and other similar media. The interwebs ain't just for basement scientists anymore. Little Andy's favorite dinosaur is 342.114-5a. Me, I like allosaurus. :-) Edit: I agree 100% with what Mark said regarding numerical categorization. Great for databasing, terrible for usage, let alone popular usage.
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