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To rephrase my question more articulately:

Speciation begins when two groups within a species starts to become reproductively isolated, and is complete when the two groups can't interbreed (for the purposes of this discussion). But then how is this possible when any time a reproductively-isolating mutation occurs in a member of that group, the member carrying that mutation could no longer breed with the other members? Therefore, speciation is theoretically a negative feedback loop. In this context, how does speciation occur?

One of the mechanisms documented by James Patton is chromosome evolution, where changes in chromosome number and shape occurred in pocket mouse and reproductively isolated the different species-complex (https://www.jstor.org/stable/2406859). But then the question still remains that the first mouse to have a different number of chromosomes would not be able to have offsprings because there are no other members with the same number of chromosomes as it does.

unless the genetics of reproductive isolation is continuous i.e. a gentically reproductively-isolated member of a species could

A. mate and have offspring with the general population but with greater cost, for instance, hybrid offspring could be at higher risk of dying in utero or be at higher risk of becoming sterile.

B. hybrid offspring, will go on to produce more offspring, still at higher cost, unless they do so with each other AND with the general population. creating a subpopulation that mates more successfully (i.e. at lower cost) with each other than with the general population.

But I have not found any articles saying reproductive-isolation is continuous rather than binary.

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    $\begingroup$ Most things in biology are continuous. Sometimes they appear to be binary due to thresholds, but it's rarely true. I would suggest reading some more about the genetics of speciation, e.g. sciencedirect.com/science/article/pii/S0960982206026649. Incomplete reproductive isolation is quite common; for example, there are various examples where offspring are sterile when male but fertile when female (e.g. ncbi.nlm.nih.gov/pmc/articles/PMC2776091). Also remember that genetics can act indirectly through behavior, which is notoriously sloppy. Or simple geographic isolation! $\endgroup$
    – Maximilian Press
    Jan 8, 2022 at 8:39
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    $\begingroup$ Concerning the continuous vs. binary question with regards to speciation, I think the concept of Ring Species may be enlightening $\endgroup$
    – acvill
    Jan 9, 2022 at 15:47
  • $\begingroup$ This is getting clearer, but is still very awkwardly worded. ——— In addition, there is an expectation that users will do research before posting, so I encourage you to check out some of the online resources available for learning more about evolution. For example, this a useful introduction to evolutionary theory from UC Berkeley. $\endgroup$
    – tyersome
    Jan 10, 2022 at 5:40

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I'd suggest looking at this article, which contains an intuitive model for how hybrid incompatibilities can arise between isolated sister taxa (i.e. populations). This criterion of pre-existing isolation is an important factor in most models.

I think that one thing that is missing from your representation of speciation is that you are assuming that every organism in a species is in one big population. This is not true. Isolation by distance is one of the simplest ways that isolation can happen.

For example, Bateson-Dobzhansky-Muller incompatibilities arise when two isolated populations of the same species each have diverged in two genes. Each change is harmless on its own, but when you put divergent allele from gene 1 from population 1 together with divergent allele from gene 2 from population 2 together, suddenly you get hybrid sterility or lethality.

Of course, the divergent alleles of gene 1 and gene 2 can't arise in the same population, for reasons you point out. Incompatibility can only evolve when these two divergent alleles arise in different populations of the same species.

For a simple isolation by distance model, imagine a river with snails (or whatever) in it. The snails at the headwaters interbreed a little with snails just downstream. Those just-downstream snails interbreed a little with headwaters snails, and also a little with the snails just downstream from them. But by the time you get to the mouth of the river, the connection between the headwater and the mouth-of-river snails is very tenuous. Now, how much of a problem is an incompatibility between headwater and mouth-of-river snails?

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  • $\begingroup$ Thank you! This made so much sense. Are hybrid incompatibilities the main driver of genetic isolation or are there other equally common mechanisms? $\endgroup$
    – AnethOthbo
    Jan 15, 2022 at 2:40
  • $\begingroup$ @AnethOthbo I think that part of my argument- which perhaps I should be clearer about- is that reproductive/genetic isolation can be achieved by many mechanisms. Probably the simplest mechanism is geography: if two people live on different continents all their lives, they will never meet and have children. If what you are interested in is cytological/molecular mechanisms of isolation, then yes, hybrid incompatibility is probably the big one. $\endgroup$
    – Maximilian Press
    Jan 15, 2022 at 4:07
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This isn't a complete or exclusive answer, but inversions can contribute heavily to reproductive isolation. A crossover within the region inverted in one homologous chromosome of a hybrid, but not the other, will typically mean one end of the chromosome is absent in the offspring, which is generally not a good idea.

Nonetheless, within the same species it is possible to have an inversion polymorphism taking up most of a chromosome. This means that you have a species which exchanges genetic material normally within most of its genome, but is divided into somewhat isolated populations in terms of that one region. (The barrier is not watertight, especially with such a large inversion, because a gamete produced by two crossovers within the inversion is perfectly normal)

This review discusses more about the general evolution of inversions and their role in speciation. (I pulled it out at random; there has been quite a bit published on the topic)

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  • $\begingroup$ While I certainly agree that inversions are an important example of an isolating molecular change, I think that the OP is asking more about how a reproductively isolating variant (such as an inversion) can arise, if it contributes to isolation- e.g. more of a theoretical and less of a cytological question. That said, your linked Kirkpatrick (2010) reference provides some helpful answers that might be worth highlighting: 1) superiority of inversion heterozygotes, 2) meiotic drive of inversions. $\endgroup$
    – Maximilian Press
    Jan 10, 2022 at 17:12

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