[08-15]

How much is large?

The dendrogram is right here: https://www.eva.mpg.de/genetics/genome-projects/neandertal/

The difference between the Denisovan and the Neanderthals is bigger than between San and French, but not by much. Keep in mind that the archaic genomes are noisy, and noise adds to their distance.

At the time, the debate was whether Neanderthals and the Denisovan constitute different species or just different subspecies. (Taxonomy is fun. You get to name species you discover after yourselves. I'd love to discover a new species, but in a pinch, a subspecies will do.)

You use the meaningless term "population". Whatever, let them be different populations. Now we have two populations, namely the "Denisovan" and the "Altai Neanderthal" living in the same cave, at roughly the same time.

[bugzz]

San and French lines have been separated by 50-100k years at least, right? So if Denisovans are more different from Neanderthals than that, why do you think the Denisovan bone was from a Modern x Neanderthal instead?

Also, if you did find a first generation Modern x Neanderthal, you'd have stretches of the genome that were 100% Neanderthal and stretches that were 100% Modern. It'd be obvious that it was an F1 hybrid. Even F2, F3 etc it'd be pretty clear. Are you saying the Denisovan genome doesn't have unique mutations?

I agree that the terms species / subspecies / populations are difficult/impossible to to define sharply.

[08-15]

No, not first generation. That would indeed show up, as it did in "Oase 1": https://www.nature.com/articles/nature14558

> Are you saying the Denisovan genome doesn't have unique mutations?

It sure does, but we don't know them. Anything unique to a single archaic individual can always be a sequencing error. (But it's high coverage! Right, but they couldn't compute proper genotype likelihoods for ancient DNA, so systematic errors end up in the final sequence.) And anything found only in Denisovans, however you define them, may or may not be fixed in them, and may or may not exist in other hominins. With so few archaic genomes, it's impossible to tell.

The actual analysis is done on variants that exist in extant humans. Which is why you never read sentence about the number of mutations unique to whoever, you always get something like "is more similar to X than to Y".

> So if Denisovans are more different from Neanderthals than that, why do you think the Denisovan bone was from a Modern x Neanderthal instead?

Distance is calculated by walking along the genome, calling a genotype for every base, and counting difference. This works well for modern humans, but for Neanderthals, a good chunk of the called genotypes are erroneous. This increases their apparent distance from humans, but it increases their apparent distance from each other even more. I'm saying, the Denisovan and Neanderthals may not really be more different from each other than French and San.

I'm not saying anything about the Denisovan in particular. I'm saying the gene flow was probably into Neanderthals, and we stumbled upon one affected individual. Interbreeding is a local event. It is easy to believe that we stumbled upon an individual that had some human ancestry. It is much harder to believe that such an individual ended up in a human population and ended up affecting the whole population uniformly.

[ummonk]

Denisovans, Neanderthals, and sapiens could all interbreed with each other without issue, and only diverged about half a million years ago, so it is only reasonable to say we’re all just different subspecies.