Modern genetic data suggests pre-humans were a group of only 1,280 individuals

Is there more discussion at your link or just the single dismissal post? Maybe I need to log in?

There are a couple of things that tend to be miscommunicated:

1. An effective population size of N means an actual population size that is significantly larger; children too young to reproduce, adults too old to reproduce, and nerds too awkward to reproduce are all not counted in effective population size.

2. If a group gets demographically wiped out at time T, their ancestors at time T-1000 vanish from the effective population at time T-1000, even though those same ancestors were part of the effective population at time T-1000 if you did the same calculation at time T-200.

(This is true to the extent that the vanishing ancestors don't also have other descendants in groups that survive. But the effect is quite significant - the effective size of the pre-Cherokee population in the year 1000 was much larger in the year 1450 than the same quantity, the effective size of the pre-1450-Cherokee population in the year 1000, is today. Was there a bottleneck? Sure; Amerinds in the region of the United States got wiped out. How long did that process take? When did it happen? We know a lot about the shape of the population over the relevant time period - is it something we're comfortable calling a "bottleneck"?)

So we might estimate our group of 1300 effective individuals as reflecting maybe 430 men of reproductive age, 870 women of reproductive age, plus 220 more women of reproductive age who fail to reproduce, 650 more men of reproductive age who fail to reproduce, and a few thousand children and elders not of reproductive age. And if this group later loses a war, their population could be a lot higher than that.

Statistics rather than intuition.

You can only judge hypotheses more or less likely in relation to each other. When you have multiple hypotheses that all explain the current situation, one may be more likely to have happened in the past than another. So if all you know is that on the first 20 tosses half were heads, you might say it's less likely the sequence was ten heads followed by ten tails, than some mix of heads and tails.

But of course, the difficult part is judging whether two hypotheses explain the same outcome. That's often somewhat subjective when it comes to historical analyses like these.

So, no, in other words, you can't draw that conclusion. Consider that in any instance where bottlenecks led to extinction we couldn't be here to discuss it, and so the only possibilities is that we won the lottery, whatever the odds were.

https://www.newscientist.com/article/dn14817-polygamy-left-i...

Mitochondrial DNA, which most people understand to be inherited entirely along the female line, is believed to point back to some single individual female “Eve” 100kya.

There are two factors at play: inheritance and mutation. If you had a large population of genetically similar individuals, you'd expect after a few gereations many parallel lineages each with their own distinct mutations.

Imagine everyone starts out with a gene that looks like AAAAAAAA; some lines would wind up with AACAAAAA while others wind up with AAAACAAA. In later generations you might see a gene like GACCATTA which came from that first group, whereas a gene like TTAACACG which came from the second (note the position of the C).

Alternatively, if you have a small population, mutations are going to accumulate in series. Perhaps you start out with some AAAAAAAA and some TTTTTTTT variants, in later generations you'd expect to find versions of the gene like AATCAGAT and AAACAGAAT which descend from the first line and TTTCAGTC and TGTCAGTT which descend from the second. The lineages' distinctness is conserved, but they both spent a lot of time developing mutations before they radiated.

Time estimates can get a little wonky because we don't really know what the mutation rate was at any given point in the past; we can kind of calibrate by sequencing genes of fossil specimens but there are only so many specimens of sufficient quality, and they only tell us which mutations had already occurred by that point in time. But the sequence of events is much clearer.

Ockham's razor says my scenario is more likely.

The bottleneck consists in the fact that the present cheetahs are the descendants of a group of 30-40 cheetahs that have lived at a certain time.

There are multiple possible explanations for why the bottleneck happened.

There might have been a climate change or another abiotic cause that has killed the other cheetahs, there might have been a disease that has killed the other cheetahs, their prey might have disappeared, another predator, like lions or hyenas might have killed most of them, and so on.

Among the possible causes, both in this case and in the case of humans, there is also the possibility that there has been, as you say, some mutation that has given to a small group an unusually important advantage, allowing them to outcompete any other cheetahs, so in time only their descendants have survived while the descendants of any other cheetahs have disappeared.

In the case of cheetahs, such a cause for the apparent bottleneck seems much less likely than in the case of humans, because it is hard to imagine a decisive advantage of the mutated cheetahs. Something like one extra meter per second in maximum speed does not seem to give enough advantage over competing predators.

The accepted explanation seems to be - by far - the simpler of the two.

Let's imagine we've got a thousand islands a million years ago, each with a thousand proto-humans living on them.

These islands live in peace and tranquility, with people occasionally swimming from one island to another to trade or visit or start a new life.

Then one year, one island decides it's had enough of peace and tranquility. It cuts off contact with all the other islands. From this point on, everyone born on that island is a descendant of only the thousand people living on that island, instead of intermingling with the neighboring islands over time, but there's still a million people.

Then, one generation, they go to war. They swim to a neighboring island, kill everyone there, and take it over, and then divide themselves between the two islands. The population drops from 1 million to 999,000. Over time, they expand to fill the two islands, and the population rises back to 1 million.

A hundred years later, they decide they need another island, so they swim to a third island, kill everyone there, and repeat.

Bit by bit, over the course of a hundred thousand years, the descendants of the original xenophobic island swim to each of the other thousand islands, kill everyone there, and repopulate.

In the genetic record, you have a bottleneck -- everyone descends from this small starting population. In the historic record, you just have a gradual pattern of migration and genocide. At no point does the population drop much below the original million; at no point does the population of pre-humans "almost go extinct".

This is the actual paper, which (presumably, I cannot access) is specifically about how they made the estimate: Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition:

https://www.science.org/doi/10.1126/science.abq7487

Then why say it's an issue?

"Hmm, this monkey looking thing isn't as tasty as a wooly mammoth, but it'll do."

(it's not like chimps don't catch and eat other primates)

It seems to me that if those lineages aren't in the DNA data, then they didn't --in the intervening years-- intermix with the lineages in the DNA data.

So, ipso facto, those lineages went extinct, and the 1280 ancestors posited in the study are the non-extinct lineages. QED.

Also, the way population dynamics work, lineages tend to die out quickly or not at all. Isolated populations can die out gradually, but it takes exceptional circumstances for a population to survive in the long term while remaining isolated.