Some basic questions about genetic variation

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That would be very strange IMO. Biologists talk all the time about the relationship between mutation and adaptation, and there are complex efforts underway, right now, to continue to understand how these are related. We’re talking about a mutation, that results from a change induced during replication, when that change was subject to correction but somehow escaped. Each of these has a nonzero probability of contributing to adaptation, but so do meteor strikes, and we don’t call those “potentially useful conflagrations.”

That’s what I mean by “precise replication.” The proofreading and correction are built in. In fact, the DNA polymerase machine includes those capabilities. It’s really not about assuming anything.

Well, the best way to understand them would be textbook-level descriptions or Wikipedia. The key player is DNA polymerase, which comprises families of related machines with different roles and properties. In bacteria, there are at least 4 different kinds of Pol, the “main” one being Pol III. All are composed of multiple parts that assemble into the final machine.

These are proteins. Proteins vary. They vary because of mutation. In principle, every single amino acid in a protein can be changed to any other. In practice, some mutations will destroy the protein utterly, some will not affect its function at all, some will affect its function only under specific conditions/circumstances, some will reduce its function in a way that the cell can live with, some will enhance its function, etc. There is nothing unique about DNA polymerases when it comes to their identity as proteins that are encoded by genes that can vary.

FWIW, some DNA polymerases are “designed” to make mistakes. A family of Pols in bacteria, called Pol IV, is called into action under highly stressed conditions and its role is to indiscriminately induce mutations, i.e., it is error-prone. (It has even been called a “mutase.”)

You are wise to reflect on how your thinking is not always well suited to initial consideration of biological questions. The existence of mutation means this, among other things: when a bacterium divides and yields two copies of itself, there is a possibility that one of those daughters is different from the original, or that both of the daughters are different. It’s one thing to know this fact; I think it takes another step to incorporate these kinds of stochastic phenomena into your basic thinking about biology, evolution, populations, etc. And yet, without converting away from law-based physics and its reliance on “types,” you’ll always struggle to think about biology.

These are open and active questions, and there is no single answer. Standing genetic variation is a fact of any population, but there are interesting and complicated relationships between mutation rate, population size, standing variation, and adaptive capacity. Your question doesn’t have a single answer.

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Thanks for asking these questions. I’m learning a lot through this thread since I don’t understand this topic, and it’s very helpful to have someone who knows the right questions to ask.

@sfmatheson Am I understanding right that you’re saying

where this reservoir existing variation ultimately came from

is an open question that doesn’t have an answer, and so the answer is currently inferred?

OR

it’s open question as to how the various relationships work together so there are various models that all yield acceptable results?

Hopefully I’m asking the question in a way that is understandable since I have so little knowledge in this area.

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We know where variation comes from. That’s the easy question. The open questions are about the contributions of standing variation, vs. “on demand” new mutations, during adaptation. There is no single “in principle” answer. We know that some species/lineages harbor immense variation and that this can be shown to be a resource for adaptation, but there are lineages where new mutation supply might be necessary.

These are not questions that have single answers. There is no one answer to standing vs. new mutation, just as there is no one answer to “what causes extinction.” And… that might be one of the most important things to learn from this thread. In biology, there is no law that says a mutation is beneficial vs. harmful. Instead, the same mutation can be either or both depending on context. That’s different from the question you’re asking but the answer reveals a very important conceptual fact about topics like this. Which is: there is no single principle that determines the answer to the question about whether standing variation, versus new mutations, or both, or neither, is required for adaptation. And that’s because every case of adaptation is unique.

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Is it easy? :rofl: Because I think I’m still confused. It comes from DNA mutations? Where does the DNA come from?

Have these lineages been specified? How do we get new mutation supply?

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Yes. It’s mutations.

That has become increasingly clear over the last few days.

Yes.

Variation in DNA comes from mutations regardless of how DNA itself came to first exist.

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Semi-conservative replication.

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Yes. Here we are thinking broadly about “DNA mutations,” since recombination and genome rearrangement are two other mechanisms that generate variation and that might not fit a layperson’s picture of a “mutation.”

I would like to answer this question but I don’t understand what you are asking. The topic here is the generation of variation and diversity within a population, so the DNA is coming from one generation and being passed to the next. If you are asking a question about the ultimate origin of DNA, that’s for another thread.

I don’t understand the question. Perhaps you are asking whether we know which lineages are the ones that don’t or can’t rely on standing variation. That’s a specific question about the literature and I can answer it but first I will ask you to try to be a bit more specific.

From new mutations in every reproductive event. In this case, because @dga471 is asking about microbes (let’s say bacteria), the new mutations come at a certain frequency constantly, all the time.

I have a suggestion that might help you and perhaps others in the conversation. Consider how you conceptualize evolution. I could be wrong but it seems that you picture evolution as a kind of developmental process in which the endpoint (humans, or modern animals, or “complexity,” for example) is a “goal.” This kind of conceptualization is very common, not just among creationists or religious people–I think it’s a natural cognitive bias in us humans. But it’s a big barrier to understanding evolution. The most basic conception of evolution, dating to Darwin/Wallace and their forebears, is selection acting on variation leading to differences. That’s all. (Yes we can and should add drift, but that’s not relevant to my point here.) This conception has nothing to do with “progress,” nothing to do with “guidance,” nothing to do with any goal or outcome. All of those things are interesting but none of them is folded into the basic idea of evolution. My hope is that by giving more thought to this basic foundational idea, which is fundamentally based on variation, you and others can get more focused on what evolutionary biology is about. And what it’s not about.

Maybe, of course, I’m wrong about the causes of your confusion. Either way, I’m glad to see the questions.

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I think it’s safe to say that things could be different.

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I’m starting to understand these differences. I looked up a few videos.

How extensively as genome rearrangement been observed?

Yes, that’s what I was asking. Maybe it’s worth starting another thread.

To know what I’m asking :rofl: I had to look up standing variation. Here’s what came up from a paper

Standing genetic variation is the presence of alternative forms of a gene (alleles) at a given locus [5] in a population. While an allele may be mildly deleterious or confer no fitness advantage over other forms under one set of environmental conditions [6], that allele may become beneficial if the environment changes.

I think I’m possibly asking which lineages can’t really on standing variation and if we know or can guess where a “jump” happened because of genomic arrangement. If that’s what’s being suggested by scientists. I don’t know if it is or not. :blush:

I get that there is no “goal” but the development obviously happened, so it’s that part that I’m having trouble getting. Hopefully that’s clear based on my questions above.

Thank you for answering them! I’m realizing it’s really fascinating - genetics appeals to my mathematical-analytical-creative brain. As a kid, for an art project, I took a tiny picture of an elephant from an encyclopedia, measured the proportions of the picture and created a grid for it, then created a grid on the paper I was working on so the enlarged elephant would be proportional, then added a background I made up. I think I’m a little weird in the way my mind does left and right brain thinking. But it may help for understanding genetics.

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Very extensively. They are common, as are larger scale mutations such as duplications of genomic segments, resulting in what are called copy-number variants.

That’s not the question, by which I mean that “jumps” due to genomic rearrangement are not somehow an alternative to reliance on standing variation. The question about standing variation is simply whether, in a particular lineage or species or adaptive opportunity, the existing variation already includes “solutions” to a “problem.” The alternative scenario is one in which “mutation supply,” from new mutation, provides solutions to the “problem.” It’s worth thinking about this before tossing in stuff about genomic rearrangement, which is just a large-scale kind of mutation.

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