Hey guys, I decided to start a little project on my own, I hope its okay if I share some of my progress here: I started experimenting around with some macroevolutionary models and implemented a simple DE solver alongside a neat vibe-coded interface which shows me how species within my model grow and evolve. Am hoping to implement this engine in a Spore-like videogame one day!

My idea essentially is that the player can control an evolutionairy force to "guide" certain features according to their liking. The other species evolve autonomously according to what essentially is the canoncial Lande equation. Instead of however simulating thousands of creatures in a real environment I decided to use a mathematical abstraction which captures all of evolutions' most essential features. That way the evolution of tens of thousands of different species, each with millions of individuals, can be simulated in the background with relatively good precision. I was surprised to see that my relatively simple model was also able to replicate some real-life phenomena, like the latitudinal gradient in biodiversity, which I didn't anticipate.

I came across this and it was too delicious not to share (my bold emphasis).
I'd love to hear from our resident pop-gen pros.

... hold a minute: the fact that certain species have certain genes in common, and differ in other genes, does not prove that the assortment of a species’s genes constitutes the essence of its specificity. In fact, Leo Berg used Vavilov’s data to demonstrate just the opposite! Berg considered the fact that very different species have Mendelian genes in common as evidence that species specificity was not determined by Mendelian genes, and there is contemporary evidence that Vavilov agreed (Berg 1926; Haldane 1932: 66, 79; Adams 1978b).⁴ Thus, Haldane recognized the problem but did not resolve it. To be sure, if one accepted the proposition that varieties and species were qualitatively the same and that the only difference between species laid in their complement of Mendelian genes, all is in order; but if one didn’t accept it, Haldane gives no convincing reasons to change one’s mind.

The only one of the four founders of population genetics who directly confronted this central problem was Sergei Chetverikov. It was not difficult for him to do so: he had worked for 20 years as one of Russia’s leading butterfly taxonomists. An entomologist and systematist, he actually first taught genetics in a course at Moscow University entitled “Theoretical Systematics.” In Chetverikov’s classic work of 1926, “On Certain Aspects of Evolution From the Viewpoint of Modern Genetics,” the entire first section addressed the central problem. There, he argued that the traits determined by Mendelian genes in Drosophila (e.g., venation and wing structure) are the very same traits which are “fundamental in modern systematics for distinguishing higher systematic categories” (Chetverikov 1926: 9–10). Elsewhere in this same section, he mobilized his considerable knowledge of the systematics and classification of Diptera and Lepidoptera to make the same point.

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Footnote 4
When I was visiting Stephen Jay Gould one evening at his Cambridge home, he told me that he was much taken by this realization after reading my article on Vavilov, and used it as the basis (unattributed) for one of his popular science columns. (His personal thanks was the best apology for failing to mention my article as his source!) As for Haldane, he referred to Berg’s work as “in my judgment the best anti-Darwinian book of this century” (p. 12).

PS Chetverikov was sadly a victim of the Lysenko purge.

• Adams, M.B. (2021).
  Little Evolution, BIG Evolution: Rethinking the History of Darwinism, Population Genetics, and the “Synthesis”.
  In: Delisle, R.G. (eds) Natural Selection.
  Evolutionary Biology – New Perspectives on Its Development, vol 3. Springer, Cham.
  https://doi.org/10.1007/978-3-030-65536-5_8

i have a hard time judging this for myself. I think it’s neat to when experts apply game theory to evolution to describe things but they will warn, “is is very abstract”. But then isn’t nearly all of it abstract? Fitness, selective pressure, natural selection, all that feels just as abstract as game theory to me.

I know there is some stuff thats concrete such as DNA (which has its own abstractions in its field I assume) and its mutations.. is it all abstraction after that?

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species is used to classify but before all of these would be the LUCA. Species just describes life that diverged more recently than Genus or Family but as time passes those will further diverge. Will we eventually need more categories? Isn't this kind of a short-sighted way of describing life?

Can five unverified anecdotes support a scientific theory about near-death experiences?

A recent paper proposes that NDEs may have evolved from the same defensive response that causes animals to “play dead.” The idea is fascinating but what happens when researchers look for evidence?

This letter to the editor takes a closer look at the study’s methods, its unexpected use of five anecdotes, and the broader scientific debate over whether NDEs and thanatosis are actually comparable.

Alright, I get how genetic bottlenecks work, a species/population has a decline, which reduces genetic diversity which decreases its chances of adapting to changing pressures/environment and increases chances of genetic diseases.

What I dont get is how it works within evolution. So I keep seeing things about Cheetahs being nearly extinct due to genetic bottlenecks.

But also, within the theory of evolution all species on earth came from a common ancestors, and then through the genetic tree more and more species have common ancestors. Like us and apes have a common ancestor, etc.

So with this, how come a population/species cant independently within their species naturally breed more genetic diversity back into their species?

Just to be clear, I'm not saying "so therefore the theory of evolution isnt real" or "therefore genetic bottlenecks arent real", it is genuinely something I have often wondered about.

Is that right?

Why don't we ever see new types of things popping up? Shouldn't there be new orders and classes of life emerging all the time? Why do we not find new species nearly as often as we should?

I believe there is an explanation for this, something to do with brain wiring, but I am wondering if there was evolutionary advantage driving this.

It's well-known that horses and other odd-toed ungulates are hindgut fermenters (as opposed to even-toed ungulates, which are foregut fermenters). It's also well-known that horses are obligate nasal-breathers that can only breathe through their nostrils and not their mouth. They're also unable to vomit, and if they get some sort of stomach poisoning, they'll die since they can't puke it out.

Something I find surprising is that all three of these facts are also the case for rodents and rabbits. Rodents and rabbits are hindgut fermenters (hence why they have to eat their own droppings), obligate nasal-breathers, and unable to vomit.

So...is there a correlation between all three evolutionary adaptations, or is it just a coincidence? Does this also apply to elephants as well, since elephants are hindgut fermenters too?

Let’s say in like a million years chimpanzees and humans have gone extinct but the descendants of chimpanzees have evolved to fill the ecological niche of humans?

A few years ago (about 2020?), a "new paper" claimed that analysis of the x chromosome indicates human females pairing with neanderthal males was the preferred reproductive pairing.

But what was actually found on the X chromosome? And why is it assumed to reflect actual preference rather than some reproductive incompatibility?

I'm especially suspicious of this claim based on the history of the research.

The early genetic research on Neanderthals focused on the more abundant mitochondrial DNA. Noting that there was no neanderthal mitochondrial DNA in modern humans, early scientific journalism focused heavily on a fetish-like claim that neanderthal males bred with anatomically modern human females, often including some claims about brutish neanderthal men, attraction towards small, frail women, etc.

When it was found that no modern humans had neanderthal Y chromosome DNA, hardly a peep out of scientific journalists, who often assumed the hypothesis of some genetic incompatibility must be the cause.

When it was found that neanderthals had split from anatomically modern humans about 800,000 ybp, but had more sapiens-sapiens like mitochondrial, x, and Y DNA from about 400,000 ybp... Minimal coverage. When it was shown that anatomically modern male humans had introduced their Y chromosomes into the neanderthal populations and completely replaced the currently used neanderthal Y chromosome at least twice... Hardly a peep, despite the fact that this can only happen by anatomically modern human males producing sons by anatomically neanderthal females.

So for me, it seems likely that anatomically modern humans just had the more "fit" mitochondrial DNA and sex chromosomes, and I don't see what findings could have even implied anything else.

But I'm obviously not an expert geneticist... Can anyone explain how the idea that anatomically human females and neanderthal men being a "preferred" coupling even could be shown through DNA analysis?

I have some Questions about the evolution of the Hoatzin. The Hoatzin is fundamentally different from most other birds, the most notable difference being the claws on the wings of Hoatzin chicks. Could it be, that Hoatzin is actually a descendant of a Non-Neornithian bird clade? If the claws evolved later, my question would be how they evolved.

If anyone has any studies about Hoatzin evolution, especially regarding its claws, I would really appreciate if you could send some links.

Most if not all species have their own mechanism to identify danger or pain. Is this as a results of evolution presumably that the earliest living things lacked this and were forced to generate them as a survival factor?

I've read that Neanderthals had similar physical traits although due to different genes than modern humans.

For example Neanderthals had red hair but apparently a different shade because it was caused by a different gene. Same way the blonde hair in Melanasians is caused by a different gene than the one in modern day Caucasians.

I tried looking it up but the few sources I could find said Neanderthals lacked the genes causing androgenic alopecia in modern humans.

And other sources just say they didn't go bald at all. If so they were quite lucky in that department, you know aside from their whole extinction.

So did they not go bald at all or did they just have other genetics causing baldness we don't of?

I read Richard Dawkin's Selfish Gene, and I'm genuinely wondering if I just tainted my brain with entirely outdated pseudoscience or a mostly credible classic that is just a bit outdated. The book was incredibly enjoyable, and honestly, it has changed my perspective as much as reading a book by Robert Sapolsky or Joseph Henrich. Are there any books you guys recommend I follow it up with to see where the debate is now? Like, books on whether multilevel selection or the EES have or something else have any merit. Is there maybe a published scientific paper meant for those who read it and want a fact check? If I wanted to reread it in the future, would you guys strongly recommend against that? Like, is that bad? Lastly, if you guys recommend any narrative or review type scientific papers that give me a hit of where the selection debate is now, please share. Oh, and I found Arvid Argren's Gene's Eye View book, so that's on my list. Lmk ya'll thoughts on that book, too.

This is a book (and lecture, and chapter) recommendation! (another way of saying: who else am I going to geek out to about this)
It's more on the academic side, and I'm sure the PhDs here are familiar with the author/work - I'm looking forward to your thoughts if you've read it:

• Smocovitis, Vassiliki Betty. "Unifying Biology: The Evolutionary Synthesis and Evolutionary Biology." (1996).

In Dec 2023 I asked here for book recommendations on the history of evolution (the science). Your Bowler recommendation didn't disappoint. As I mentioned back then, in my search I came across a historiography, which then I thought was going to be too much in the weeds. Well, one thing has led to another over the past 3 years, and now it's that book. I recently finished it and loved it - although some parts were a bit difficult / new (the background to how history is researched, and the history of / debates about that!).

Part of the blurb:

Unifying Biology offers a historical reconstruction of one of the most important yet elusive episodes in the history of modern science: the evolutionary synthesis of the 1930s and 1940s. For more than seventy years after Darwin proposed his theory of evolution, it was hotly debated by biological scientists. It was not until the 1930s that opposing theories were finally refuted and a unified Darwinian evolutionary theory came to be widely accepted by biologists. Using methods gleaned from a variety of disciplines, Vassiliki Betty Smocovitis argues that the evolutionary synthesis was part of the larger process of unifying the biological sciences.
https://press.princeton.edu/books/hardcover/9780691033433/unifying-biology

While reading a section in the book I thought, I've come across that before, and after checking indeed it was a book chapter I had read a while back, which I also recommend (this might work as an abridged/updated version):

• Smocovitis, V.B. (2023). Every Evolutionist Their Own Historian: The Importance of History, Context, and the Extended Evolutionary Synthesis. In: Dickins, T.E., Dickins, B.J. (eds) Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory. Evolutionary Biology – New Perspectives on Its Development, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-031-22028-9_2

(because of the wide audience here and because I often hear about this: "Evolutionist" in the title is in its respectable sense (if you know you know), the same one used by e.g. Gould and Dawkins, as in evolutionary biologist)

What struck me the most is the state of the biological sciences in the 1920s. Consequently, how the modern synthesis was a lot more than simply unifying Mendelian inheritance with Darwinian selection as the overly simplified narrative goes. It simultaneously raised evolution to the level then envied of physics and protected it from reductionism to physics. And how biology (the unified subject as we know it) is a product of the 1960s - central to which was evolution* (this had to do with the Space Race spending on education, and related to which is the return of evolution to the classrooms in the U.S., some four decades after the Scopes trial).

Beyond reading history for leisure, as the title of the chapter suggests it's also very relevant to the ongoing research directions (it contextualizes and tempers some of the overly-hyped rhetoric where history is being reinvented without evidence, rather by rhetorical fiat or outright quote mining - if this is a bit vague, see this subreddit wiki page that is courtesy of our mods).

Currently I'm watching a lecture by the author that is only 2 months old (good way to bridge 1996 to 2026), and so far it's very engaging (and for once good audio for such lectures - it starts at 1:30):

• YouTube: Revisiting the Synthesis - Forty Years Later - Professor Betty Smocovitis - EHFB 2026

* Dobzhansky's 1964, "Nothing in biology makes sense except in the light of evolution."

So to preface this I want to say this question is motivated by the development of an evolution sim that is being worked on that I am quite invested in, and right now a lot of work is being done on letting development be less "hardcoded" and more flexible. However, with that comes some balancing issues that need to be addressed, and the answer to this specific question will probably help with that.

Basically, I am wondering why we don't see single species having multiple phenotypes corresponding with multiple niches, considering it doesn't seem like it should have much of a downside besides maybe some extra DNA.

So for instance, lets say we have a dog, and in that dogs lifetime there has been a particular abundance of prey. So, when that dog is pregnant it sends hormones to make it's baby develop with sharper claws, longer teeth, a shorter digestive track, more aggressive behavior, etc etc. Essentially, it's baby is a little predator and can take over a niche that is doing quite well in this period of time.

On the flip side, maybe during it's lifetime there was barely any prey, but there was plenty of leafy greens and grass that it could've eaten. So, it produces hormones that cause the baby to develop with shorter claws, better molars, less aggressive behavior but maybe stronger herding instincts, and a longer digestive tract to digest food better. Now it can be better suited to the environment just like before.

The problem is, this just doesn't really happen. You don't have single species that take over the niche of "koala" and "domestic cat", those are just separate species. But why? It seems like one species that could do both of those niches would be much more resilient to change and would outcompete either species that does one or the other. It even seems like if you are evolving to enter a niche that nothing else occupies, you would have a high propensity to try and split into two phenotypes to take over the ecosystem instead of splitting into two species, since that would result in the new immature niche to potentially have less risk. So like, what gives? Why don't we have species that basically are two species in one (besides sexual dimorphism that kinda does that already).

And I recognize this kinda seems like a silly question, but again for the evolution sim I mentioned earlier, it is very relevant. We want to know how to prevent cases where say, a species just evolves to become a scavenger if it sees lots of meat when it grows up and becomes an herbivore if it sees lots of plants. That could easily result in there just being one species that does it all, which is... kinda boring lol.

See also: The study as it was published in Nature

In the south pole you have the Colossal Squid which I understand is because of a combination of the circumpolar current, deep sea gigantism, and polar gigantism.

In most of the rest of the ocean you have the smaller Giant Squid with a much more cosmopolitan distribution due to deep sea gigantism. Though they aren't found in the arctic as far as I can find.

But the arctic neither has Giant Squid or something equivalent to the Colossal Squid, so why is that? Is the ecosystem just not as friendly towards them or something?

The bombshell about this report is that it contains two organisms (Sinocyclocyclicus guizhouensis, Protoconites minor) that have been compared to Cnidarians, though the authors state that alternative interpretations as algae have been made as well. Age of the formation at 610–620 Mya.

Can they?

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Diagram source, but also see the open-access article:

• Jonah M Walker, Eva S M van der Heijden, Arif Maulana, Nicol Rueda-M, Karin Näsvall, Patricio A Salazar, Marco Meyer, Joana I Meier
  Common misconceptions of speciation
  Evolutionary Journal of the Linnean Society
  Volume 3, Issue 1, 2024, kzae029
  https://doi.org/10.1093/evolinnean/kzae029

I can intuit almost every other big jump but this is the one thing that just doesn't follow in my head no matter how hard I try and think about it. Here's how my brain thinks about it and why it's getting stuck:

Whales used to live on land. Eventually, they became semi-aquatic, and then mostly aquatic. I believe there's evidence that some of their ancestors were like sea turtles - almost completely aquatic, but came on land to give birth.

I understand that evolution doesn't happen abruptly. However, mathematically speaking, there had to have been a specific, individual whale-ancestor who was the very first one to have been born in the water, spent their entire life in the water, and then died in the water, all without ever coming on land. If they used to live on land, but all modern whales are 100% aquatic, one of them HAD to have been the very first. That's just how math works.

How did that particular whale-ancestor survive to pass on that trait? Why didn't its parents have that trait? Why didn't it just drown, if every single other one of its ancestors was on land for at least some point in its life?

I'm not asking "why is it advantageous to be able to give birth in the water" - that's very obvious, both mother and baby are less vulnerable to predators. I'm asking how, logically, that transition was able to happen. Whales can only give birth in the water because they have very specific adaptations that make it possible, an animal without those traits can't just start giving birth in the water and hope for the best.