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I clearly recall reading that DNA-based phylogenetic analysis indicated that primates and rodents have common ancestors that are more recent than common ancesto

I clearly recall reading that DNA-based phylogenetic analysis indicated that primates and rodents have common ancestors that are more recent than common ancestors with other mammals. So in that sense, rodents are more closely related than, for example, dogs, cats, cattle, etc. Pigs I may be wrong about. They're clearly more similar than dogs, cats and cattle. In embryonic development, for sure, and I remember that from dissecting a fetal pig. And there is the saying that embryology recapitulates phylogeny. But a quick search didn't come up with any DNA-based phylogenetics. As you say, "traditional taxonomy is bad at determining how related species are". It's largely based on morphology, embryology and fossil evidence. But that can be irffy, given the thin fossil record, and the common occurrence of independent selection. DNA-based classification is really the only way to get objective phylogenetic trees. And as we get them, we learn that lots of classical taxonomy is just wrong. And that's why reading about taxonomy online is so confusing. It's a mix of old and new, with lots of more-or-less uninformed speculation.

thaumasiotes 8y ago
> Pigs I may be wrong about. They're clearly more similar than dogs, cats and cattle. In embryonic development, for sure, and I remember that from dissecting a fetal pig. And there is the saying that embryology recapitulates phylogeny. But a quick search didn't come up with any DNA-based phylogenetics. The saying exists, but it is not based in anything other than wishful thinking. Ontogeny does not recapitulate phylogeny; that saying is the tongue map of evolutionary analysis. https://en.wikipedia.org/wiki/Recapitulation_theory https://en.wikipedia.org/wiki/Recapitulation_theory > the shortcomings of the theory had been recognized by the early 20th century, and it had been relegated to "biological mythology" by the mid-20th century. This did not prevent its propagation into the 21st century in a variety of biology textbooks. If you believe the page on euarchontoglires, you can see that pigs cannot be more closely related to humans than dogs, cats, and cattle, because all four of those human-other pairings have exactly the same common ancestor, the common ancestor of the euarchontoglires (the tree branch containing humans) and the laurasiatheria (the branch containing pigs, cattle, cats, and dogs). Any closer "similarity" between pigs and humans in specific is not driven by their evolutionary relationship. > DNA-based classification is really the only way to get objective phylogenetic trees. And as we get them, we learn that lots of classical taxonomy is just wrong. DNA-based classification is not conceptually different from morphology-based classification. They are both directly premised on the model of "descent with modification". DNA-based classification is generally superior because there is more information in the DNA than in the morphology. (Or at least, we recognize more information in the DNA than we do in the morphology.) But morphology-based classification did nearly 100% of the work of establishing modern taxonomy, and overwhelmingly DNA-based analyses confirm the existing morphology-based conclusions. > traditional taxonomy is bad at determining how related species are This is true in the sense of assigning a cardinal number to the relationship. ("Diverged 80mya.") It is false if your goal is only to assign an ordinal number. ("Humans are closely related to baboons, distantly related to rabbits, and remotely related to elephants.") The same objection applies to DNA-based taxonomy; we get cardinal numbers by assuming a particular constant-rate molecular clock, but the raw conclusions of DNA analysis are entirely ordinal. > as we get them, we learn that lots of classical taxonomy is just wrong. (quoting again to respond along another topic) Notwithstanding the overall massive success of traditional taxonomy, there are some obvious weak points. They tend to derive from philosophical beliefs of the biologists rather than from failures of the morphology-comparing model. Two major biases that I'm aware of are the historical belief that taxa at the same level should include roughly the same number of extant species -- this was featured in a "teach the controversy" sidebar in a college biology textbook of my mother's -- and the stronger view that genera should contain more than a single species. Since the groupings prompted by these beliefs were not even intended to "cleave reality at the joints", it's not so surprising that they suffered under more objective analysis.
- mirimir 8y ago
  OK, I've largely conceded re pigs. But do you agree that there's a good case that rodents are more closely related to primates than most other mammals are? Or do you believe that the evidence is too weak? I could do some serious literature research, I suppose. But I didn't really set out to write a review.
  - thaumasiotes 8y ago
    I have nothing against the claim that rodents are closer to primates than other mammals are. I don't think that goes a long way toward explaining the use of mice in labs; it would be an equally strong argument for using gerbils, rabbits, capybaras... I think mice are used because they're small and easy to keep, and because by now there's a lot of lab-mouse-specific infrastructure -- existing literature about them, special strains of mice bred for use in the lab, and so on. https://en.wikipedia.org/wiki/Laboratory_mouse#History_as_a_biological_model https://en.wikipedia.org/wiki/Laboratory_mouse#History_as_a_... suggests (in my eyes) that the use of mice is basically a coincidence. The fact that they're at least as closely related to humans as other similarly cheap, non-dangerous animals is a plus, but I don't think it was the reason mice were used historically and I think it's only a minor contributor to the continuing use of mice today. When you're really hoping to transfer a finding over to humans, you use monkey models, though I understand those are getting rarer under a combination of cost and animal-rights-activism issues.
    - mirimir 8y ago
      From an historical perspective, I totally agree. Decades ago, when scientists settled on the mouse model, I don't believe that there was much (if any) solid evidence about evolutionary relatedness. As you say, mice were used because they were the least-expensive mammalian option. Even so, it's arguable that predictive success for the mouse model helped drive its widespread adoption. Even so, just about all small mammals (e.g., rodents, shrews and moles) are more closely related to primates than large mammals. So maybe it was inevitable. > ... getting rarer ... Funny story. I was a grad student in the late 70s. And there was an animal-rights riot on campus. The primate lab was besieged. And some of us, whose thesis research depended on our building's mouse colony, were totally freaked.

thaumasiotes 8y ago

> Pigs I may be wrong about. They're clearly more similar than dogs, cats and cattle. In embryonic development, for sure, and I remember that from dissecting a fetal pig. And there is the saying that embryology recapitulates phylogeny. But a quick search didn't come up with any DNA-based phylogenetics. The saying exists, but it is not based in anything other than wishful thinking. Ontogeny does not recapitulate phylogeny; that saying is the tongue map of evolutionary analysis. https://en.wikipedia.org/wiki/Recapitulation_theory https://en.wikipedia.org/wiki/Recapitulation_theory > the shortcomings of the theory had been recognized by the early 20th century, and it had been relegated to "biological mythology" by the mid-20th century. This did not prevent its propagation into the 21st century in a variety of biology textbooks. If you believe the page on euarchontoglires, you can see that pigs cannot be more closely related to humans than dogs, cats, and cattle, because all four of those human-other pairings have exactly the same common ancestor, the common ancestor of the euarchontoglires (the tree branch containing humans) and the laurasiatheria (the branch containing pigs, cattle, cats, and dogs). Any closer "similarity" between pigs and humans in specific is not driven by their evolutionary relationship. > DNA-based classification is really the only way to get objective phylogenetic trees. And as we get them, we learn that lots of classical taxonomy is just wrong. DNA-based classification is not conceptually different from morphology-based classification. They are both directly premised on the model of "descent with modification". DNA-based classification is generally superior because there is more information in the DNA than in the morphology. (Or at least, we recognize more information in the DNA than we do in the morphology.) But morphology-based classification did nearly 100% of the work of establishing modern taxonomy, and overwhelmingly DNA-based analyses confirm the existing morphology-based conclusions. > traditional taxonomy is bad at determining how related species are This is true in the sense of assigning a cardinal number to the relationship. ("Diverged 80mya.") It is false if your goal is only to assign an ordinal number. ("Humans are closely related to baboons, distantly related to rabbits, and remotely related to elephants.") The same objection applies to DNA-based taxonomy; we get cardinal numbers by assuming a particular constant-rate molecular clock, but the raw conclusions of DNA analysis are entirely ordinal. > as we get them, we learn that lots of classical taxonomy is just wrong. (quoting again to respond along another topic) Notwithstanding the overall massive success of traditional taxonomy, there are some obvious weak points. They tend to derive from philosophical beliefs of the biologists rather than from failures of the morphology-comparing model. Two major biases that I'm aware of are the historical belief that taxa at the same level should include roughly the same number of extant species -- this was featured in a "teach the controversy" sidebar in a college biology textbook of my mother's -- and the stronger view that genera should contain more than a single species. Since the groupings prompted by these beliefs were not even intended to "cleave reality at the joints", it's not so surprising that they suffered under more objective analysis.

mirimir 8y ago
OK, I've largely conceded re pigs. But do you agree that there's a good case that rodents are more closely related to primates than most other mammals are? Or do you believe that the evidence is too weak? I could do some serious literature research, I suppose. But I didn't really set out to write a review.
- thaumasiotes 8y ago
  I have nothing against the claim that rodents are closer to primates than other mammals are. I don't think that goes a long way toward explaining the use of mice in labs; it would be an equally strong argument for using gerbils, rabbits, capybaras... I think mice are used because they're small and easy to keep, and because by now there's a lot of lab-mouse-specific infrastructure -- existing literature about them, special strains of mice bred for use in the lab, and so on. https://en.wikipedia.org/wiki/Laboratory_mouse#History_as_a_biological_model https://en.wikipedia.org/wiki/Laboratory_mouse#History_as_a_... suggests (in my eyes) that the use of mice is basically a coincidence. The fact that they're at least as closely related to humans as other similarly cheap, non-dangerous animals is a plus, but I don't think it was the reason mice were used historically and I think it's only a minor contributor to the continuing use of mice today. When you're really hoping to transfer a finding over to humans, you use monkey models, though I understand those are getting rarer under a combination of cost and animal-rights-activism issues.
  - mirimir 8y ago
    From an historical perspective, I totally agree. Decades ago, when scientists settled on the mouse model, I don't believe that there was much (if any) solid evidence about evolutionary relatedness. As you say, mice were used because they were the least-expensive mammalian option. Even so, it's arguable that predictive success for the mouse model helped drive its widespread adoption. Even so, just about all small mammals (e.g., rodents, shrews and moles) are more closely related to primates than large mammals. So maybe it was inevitable. > ... getting rarer ... Funny story. I was a grad student in the late 70s. And there was an animal-rights riot on campus. The primate lab was besieged. And some of us, whose thesis research depended on our building's mouse colony, were totally freaked.