Phylogeny - Help me see what you see

Conversation
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I am quite sure that the vast, vast majority of biologists would agree that the sequence differences between and within species is due to mutations that happened at some point in history. If we compare the same gene from chimps and humans and see differences the cause of those differences is mutations.

Those would be the mechanisms that affect which mutations make their way into modern populations. They generally boil down to why some lineages thrive and proliferate while others shrink and go extinct. They can include modes of speciation, or even selective pressures that are promoted or limited by developmental processes.

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In my experience, scientists start with the observations they want to explain and then attach words to the categories the observations fall into. Non-scientists seem to start with the words and then force the observations into those definitions. The first step would be to start with the observations.

One of the sets of observations I mentioned before is sequence divergence. If we narrow down into the causes of why species have different sequences in their genome then it makes a lot of sense to say that microevolution blends right into macroevolution. If you start with a common ancestor and track the genome sequences of every generation in each lineage you would see a generation by generation accumulation of singular mutations. 2+2=4.

However, if I am talking about why speciation happens, or why some clades become more numerous, then it doesn’t make sense to talk about the accumulation of mutations. In this setting we might define microevolution as natural selection of alleles within a gene pool. Macroevolution would be the process that creates two separate gene pools. In this case, microevolution does not add up to macroevolution because macroevolution has the added mechanisms of speciation. We could also talk about clade selection where whole groups of species are selected for. Once again, in that specific case it wouldn’t make sense to say microevolution adds up to macroevolution.

Getting back to the thread, we were specifically talking about what creates the differences between genome sequences in different species. In this case, microevolution does add up to macroevolution.

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First, I am not speaking for myself. I am reporting what evolutionary biologists themselves have said. I am not saying who is right or wrong, but merely reporting that differences of opinion exist.

It is as if someone said: “Philosophers say that there is no free will” and I responded: “There are some philosophers who would disagree with that.” The report that some philosophers disagree would be correct – which is a completely different question from whether those philosophers were right to disagree.

John Harshman (who has a doctorate in phylogenetics or a related field, I believe) agrees with me that such differences of opinion exist. If you read what he wrote above, you will see:

You seem to be saying that John Harshman is wrong, that there is complete unanimity among evolutionary theorists on this question. You seem to be saying that he does not understand the meaning of the evolutionary theorists that he reads. I will let you take up this disagreement with him; perhaps you know the literature better than he does, and you can show him where he does not understand what he has read.

Second, regarding the question of various levels of mechanism in evolution, I again suggest you ask John Harshman about this. He can speak your language better than I can. At one point he told us something about gene regulatory networks, and how changes to those networks can be responsible for some evolutionary change that mere point mutation plus drift plus selection does not achieve. I am not clear on the details. I would suggest that you ask him to explain what gene regulatory networks are and how they figure into evolutionary change.

Note that nothing I have said here has anything to do with defending any conclusion of design or denying the existence of macroevolution. I merely mentioned that not all evolutionary theorists agree that the whole course of evolution can be explained as a simple sum of incremental changes at the level of mutations to DNA. I still believe that this claim is correct, as a report of the differences in expert opinion that are out there.

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No, I don’t think so. Saltation is not what anyone means by macroevolution. Instead of macro and micro events or results, it might be better to think of macro and micro processes. Microevolutionary processes are mutation, selection, drift, and a couple others, all involving a change in allele (or some genetic feature) frequencies in a population. The main example of a macroevolutionary process is species selection, which involves no change in allele frequencies in any population. Consider for example the K/T extinction, which seems to have preferentially eliminated large terrestrial animals, leaving only small ones. I wouldn’t consider that “deeper”, just different.

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Alright then. Produce a citation from these evolutionary biologists you report from showing that mutations cannot produce “major changes” (whatever that means)? As well as examples of those major changes?

That’s one giant strawman.

Another strawman. I never said anything about “levels of mechanism in evolution”. You missed it from the start.

You argued that it appears something changes at deeper level (which is not mutations, drift etcetera) leading to evolution and I replied that was false as the most basic level at which evolutionary forces can act is DNA or RNA. There is nothing deeper than that in the context of the ingredients needed for evolutionary change.

Gene regulatory networks are comprised of cis-regulatory modules and genes. They are all DNA and as you know, DNA is subject to mutations. If these mutations are harmful, purifying selection kicks in to weed out the deleterious variant, otherwise positive selection keeps the adaptive variant. A variant could equally get lost or fixed by genetic drift. DNA is the most fundamental level at which evolutionary forces can act.

I agree. However, as others have pointed out, biological differences within (human-human) and between (human-chimp) species are due to the accumulation of mutations over generations.

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I wasn’t speaking of saltation, nor did I say that saltation was what anyone meant by “macroevolution.” Let me try again to say what I meant.

Remembering way back, to a discussion of several months ago, where we touched on the topic of micro/macro, I had thought you said that while point mutations, selection etc. were responsible for much or all of microevolution, other parts of evolution were caused by “changes in gene regulatory networks.” I took it, perhaps wrongly, that a “regulatory network” would be a complex entity with many interacting components, that it would tend to be conserved over time, and that changes in its composition would be the result of something more than the occasional random knocking-out or addition of a nitrogenous base. So I thought you were saying that there were two parallel processes, one the routine mutations to the DNA chain, which mutations are then subject to selection etc., and the other the operation of gene regulatory networks, which change, when they do change, due to causes which go beyond routine mutations to the DNA chain. And I’m trying to relate that to your remark above.

So perhaps you can clarify. You have said that I was correct in noting disagreement among evolutionary theorists regarding the relationship between micro and macroevolution. Those evolutionary theorists who think that macroevolution is not just repeated rounds of microevolution – do gene regulatory networks have any place in their reasoning? If not, what are they thinking of when they say that macro is not just repeated rounds of micro?

In answering this last question, you will also be answering Michael Okoko’s request for an example of evolutionary change that (according to some) isn’t fully accounted for by the usual mutation, selection, etc. business.

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I said no such thing. Changes in regulatory networks result from mutations to DNA sequences, nothing else. There is no special “change in regulatory networks” mechanism separate from microevolutionary processes. You might find a biologist willing to make such a claim, but that person would not understand evolution. @Michael_Okoko is entirely right about this.

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Again, I never said any such thing.

Yes, regulatory networks are complex. But no, changes to them aren’t any different than any other mutations, chiefly insertions, deletions, and point mutations. And they become fixed in the ordinary way too, through selection and drift. I don’t know what I could have said to make you think otherwise.

Conceivably some of them think so, but if so they don’t understand what I said above.

I already answered that several posts ago: species selection, which doesn’t change anything in any population’s genome but can radically change the composition of a biota in a very short period of time, as in the K/T mass extinction.

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@Eddie I never denied species selection or its ability to induce evolutionary change. I was refuting your claim that evolutionary forces can act a level deeper than DNA or RNA. Species selection in a broad sense is an evolutionary force like natural selection or drift, and it acts on DNA (although not in the same way as the former two) as well.

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@Eddie it seems to me you keep getting this thing with macro vs microevolution wrong based on some fundamental misconception you have. You can correct me here, but apparently you think that there are scientists who think some evolutionary transitions required something other than mutations subject to various population genetic processes such as selection and drift. I gather that you probably think this means there are some evolutionary changes that are either so big or so strange that God has to intervene in the process of evolution, or at least you want to argue in a way that appears to keep the door open to this idea.

But since you don’t appear to have read the authors you’re quoting with any comprehension (or not actually read at all), you’re not aware that what is being talked about with respect to macroevolution in those quotes you some times bring.

You appears to think that what is being talked about with the term macroevolution is something like a large-scale morphological and/or ecological transition. Say, when fish evolved into tetrapods, or when terrestrial mammals evolved into whales. I get the impression that you believe that the authors you quote think that kind of macroevolution can’t be reduced to the accumulation of microevolutionary change. That “Big Evolution” can’t result from just lots of “small evolution”.

But those are not actually what the authors you and Paul Nelson like to quote, are talking about in those quotes. There are different concepts that the word macroevolution can refer to.

The authors you’ve referred to are NOT speaking about the changes observed in some lineage whereby an ancestral population evolves anatomically and genetically into a descendant, but refers instead to things like the rates of extinction and speciation during different periods in life’s history. Species selection patterns for example. These are macroevolutionary patterns too.

One can ask a question such as “Why, during this period in the Ordovician, did these particular evolutionary divergences occur, and these other lineages go extinct at such high rates?”.
This is a question about a macroevolutionary pattern, and the explanation can owe to (for example) a combination of environmental factors affecting many species simultaneously, such as changing climate, or geological processes that break up a continent.

Or there could be simpler geographical causes at the level of species range. A species might have spread out over a very large area, and thus inadvertently ensure the future success of the species simply by the fact that it is unlikely for any environmental catastrophe, or period of change, to completely eradicate the species over such a large area. Such phenomena can contribute to an explanation for why some species have fared well and both speciated a lot, and seeded many smaller populations which frequently went extinct.

Or there could be a genetic component to that explanation, for example that organisms with certain traits fared much better because they were very plastic on evolutionary timescales, while others became genetically entrenched and unable to change much, leading eventually to the extinction of organisms with those traits as they did not possess the ability to adapt quickly enough to changing circumstances.

It is these macroevolutionary patterns that potentially aren’t explained merely as the accumulation of microevolutionary changes.
Why some clade of organisms went extinct because they had become poorly adaptable or too specialized, and why some other clade of organisms was very successful because they had retained a high level of pasticity or were successful generalists - is not explained merely by saying that mutations accumulated and these were subject to natural selection and genetic drift.

Or because some species colonized a much greater geographical range (which again could be facilitated because they were generalists instead of specialists, or were genetically more plastic).

But nowhere in this debate over micro vs macroevolution within paleontology and evolutionary biology is it implied that when some ancestral population evolved anatomically and genetically into a descendant over some geological peroid of time, that this did not occur by the accumulation of microevolutionary changes. No, those are still just mutations subject to selection, drift and so on.

Have I clarified matters at least a bit here?

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@John_Harshman and others,
What are the mechanisms that enable genetic plasticity?

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I don’t know if this is an example of what @Eddie is talking about:

If so, I don’t think it is quite accurate to say this indicates that serious evolutionary biologists consider there to be “deeper” mechanisms involved in macroevolution beyond the microevolutionary processes such as mutation, selection and drift. Rather, Haig seems to be operating at the higher, theoretical level of the abstractions and language we use to understand the evolutionary process.

There are, of course, some not-so-serious people who are technically biologists and insist that there are “deeper” mechanisms that involve some invisible, spooky “designer” doing some mysterious stuff that causes macroevolution. But, as I said, these are not serious thinkers and, in any event, @Eddie has reassured us he is not necessarily referring to them.

I found this interview with Haig interesting, though not entirely convincing or (admittedly) always comprehensible:

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I think basically modularity without a lot of co-dependence entables plasticity. That no, or only few distinct modules really integrate into earlier evolved modules so they become co-dependent.

You can have a core module (CM) that other external modules depend on, but if the function of the core module becomes integrated with the function of external modules and they become co-dependent on each other for function, then they can tolerate less change before they start negatively affecting each other.

plastic vs rigid network
plastic vs rigid network1604×762 132 KB

In this figure, under a case of low plasticity you could only change or lose external module E3 and E5 without it affecting the function of anything else. Whereas in the case of high plasticity, E1, E3, and E6 can be lost or changed without anything else being affected. In addition, the core module does not depend on any of the external modules for it’s function, so they can all effectively be lost or replaced.

It is not that change of the low plastic state is impossible, it just requires more steps, and as such is slower to adapt compared to the highly plastic state. For example, in order to imagine changing the function of E1, you’d need the entire E1 module duplicated so one or more of such duplicates can continue to function while E1 then becomes more open to change without negatively affecting the functions of E2, E6 and the core module. I think this picture also helps explain why something like whole genome duplication enables a lot of evolutionary potential.

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But wouldn’t that just be an example of the alleles that lead to animals being very big and living on land being removed from the population due to selection pressures?

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No. What do you mean by “the population”? We’re talking about the extinction of many species without any changes in allele frequencies in any of them. This is the biota, not “the population”.

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https://reader.elsevier.com/reader/sd/pii/S0012160616000166?token=0162B790EE48EF6B4FB8C7CB7F0107B4E0E5CBCE545D762A3F348328788ED73AE6EC9722C851F67177EEC1E95B6EAF28

The last URL is open access. It is an interview by science historian Ute Deichmann with the late Eric Davidson (d. 2015), dealing in part with Davidson’s dissent from textbook neo-Darwinian theory (micro → macro). See p. S25:

Eric: Since the body plans are made by development, when you consider evolution of different kinds of animals, it means their developmental process is different. How else can you think about it? Darwinian evolution was of a completely different kind. It was all about small changes and they felt if you could understand changes in petunia colors, you could understand changes in whether animals have heads or not. And that’s just total nonsense. But you can’t really blame the Darwinians, because all of Darwinian theory, from the Neo-Darwinian synthesis of the 1930s, was built in the absence of, and ignorance of, any knowledge of how development actually works. Other than wrong theoretical ideas. And in the absence of any knowledge about how transcription works and in the absence of any knowledge about anything that has to do with how the processes of life that make animals actually occur. So it couldn’t possibly have been right, and it wasn’t.

Ute: But the problem is that neo-Darwinians did not include the growing knowledge about development later on.

Eric: Now, that’s what I was going to say. Where you can fault them is that they didn’t learn. That they stuck their heads in the sand, and ever since they have been like ducks with their heads stuck in the sand. So it’s been necessary to start over again, considering the nature of evolutionary process. It has pervaded every aspect of evolution. How do we interpret the fossil record? What happened? How do we interpret the real-time changes in rates of evolution?

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None of that is relevant to the distinction between micro and macroevolution. There is not any thing in those quotes or papers which say that the changes that occur between ancestor and descendants that give rise to different morphologies or behaviors, aren’t the accumulation of genetic mutations subject to genetic drift and natural selection. You seem to have brought quotes that speak about the magnitudes of change that these mutations result in, and whether to call that “gradualism” or “saltational” evolution. Of course, since there is no actual scale on which these terms have been rigorously defined, the debate is rather pointless.

At what magnitude of incremental change does something cross over from a “gradual” to a “saltational” step?
innovations vs variations

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I dislike these drive-by postings of yours. Unless you’re willing to engage with the topic, don’t post. Now, what in any of those links is a response to what I said, and why?

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Thank you for clarifying. Clearly I misunderstood what you were saying in that older discussion.

That example would explain the massive destruction of species or groups. It wouldn’t explain, e.g., the generation of dozens of new phyla in a (relatively speaking) short period of geological time.

Look, I am not wedded to these terms, macroevolution and microevolution. I could do without them. I’d be quite happy to talk about causes of major structural change vs. causes of minor structural change. It was my understanding that some evolutionary theorists think that the rise of major structural changes is not easily explained by the usual stuff (random mutation, drift, selection) and awaits really good explanation. Thus, we see phrases like “the problem of the rise of novel organismal form.”

I’ll give you a quotation that is just one of many I seem to keep stumbling across. It comes from an evolutionary theorist who is neither a creationist nor an ID proponent, and for all I know, an atheist or agnostic. Since everyone here appears to be claiming to be very knowledgeable about evolutionary theory today, they should recognize the author without my naming him or her. Here it is:

“… the puzzle of how new phenotypes come into being has stymied science for more than a century. It’s one thing to recognize that phenotypes are like enormous pointillist paintings, created one molecular change at a time. It’s another to use that insight to understand how those paintings are actually created. The challenge is daunting … Referring to random change, recited like a mantra since Darwin’s time, as a source of all innovation is about as helpful as Anaximander’s argument that humans originated inside fish. It sweeps our ignorance under the rug by giving it a different name. This doesn’t mean that mutations don’t matter, or that natural selection isn’t absolutely necessary. But given the staggering odds, selection is not enough. We need a principle that accelerates innovation.” [emphasis added]

It is statements like this that I have in mind. I am quite willing to drop the whole micro/macro language, and ask instead, “How are major changes in organismal form produced?” It’s fine to say, as Michael Okoko is saying, that these changes will involve changes in DNA. No one is denying that. But clearly, some evolutionary theorists think that “a principle that accelerates innovation” is necessary to explain the speed of major evolutionary change. And I don’t think that for these theorists “a principle that accelerates innovation” means “waiting indefinitely until a useful mutation happens to come along, so that selection can act on it.” That wouldn’t “accelerate innovation” at all.

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OK, got it.