Morphologically, it makes a lot of sense for later Indonesian samples like Ngandong to be southern Denisovans. Some of my work from 25 years ago focused on the morphological connections of Ngandong and early Australian skeletal samples. The finding of Denisovan ancestry in Papua and Australia makes this seem like a logical explanation. The Ngandong and Sambungmachan samples have substantially larger brain size than earlier Trinil-Sangiran samples, and a Middle Pleistocene introduction of a new Denisovan group might explain that.
Putting the Papuan-Philippines Denisovan ancestors into a geographic space is challenging if they are not Ngandong-like. If H. erectus was sitting on Java until 100,000 years ago, where were the Denisovans? It's hard to accommodate this problem with a double-dispersal after 100,000 years ago (Denisovans, then modern humans) because of the evidence for deep diversity in Indonesian Denisovans.
The reason to think that Ngandong is H. erectus and not Denisovan is the extent of shape similarity between this sample and the earlier Sangiran and Trinil material. Potentially that might be compatible with some superarchaic (=Sangiran erectus) contribution to the Indonesian Denisovan branch. Still, in the absence of DNA most assumed that there was a strong ancestry component in Ngandong from Sangiran. This is why Ngandong has been called H. erectus by so many people. But it is valuable to remember that they were seen as much more modern than Sangiran even at the time of their discovery.
Regarding the timing of superarchaic introgression, Rogers' most recent work still suggests a double contribution. The common ancestor of Neanderthal and Denisovan branches received close to 5% superarchaic, the Denisovans later received a smaller fraction, something like 2%. This model is also replicating the 2% Neanderthal-modern and 6% modern-Neanderthal fractions from other work, so I think it's tracking pretty well. The timing of the first pulse of superarchaic was then prior to 700,000 years ago. The Denisovan-specific superarchaic introgression is hard to date. So far all of the approaches for quantifying that introgression are relying on binning SNP counts and not linkage.
We would know more if we had better estimates of superarchaic fractions within the introgressed Denisovan components of living people. But it's admittedly a challenge to sort out the two Indonesian deep components. As far as I can remember, no one has looked hard at those Indonesian components to ask whether the appearance of two deep branches might instead be some superarchaic-mixed signal.
>later Indonesian samples like Ngandong to be southern Denisovans
I think it makes a perfect sense. It looks now that Denisovans were present and much diversified in Asia for a very long time, and it is very likely they swamped Erectus completely long ago, except maybe for small refugia islands like Flores.
I recall also an article by Wolpoff (your former advisor?) regarding continuity between Australia (Willandra lake) and SEA erectoid samples, which in light of what you wrote are likely of Denisovan lineage.
Interesting! There are some potential nomenclatural ramifications if this is true. If Zhoukoudian and Denisova and Harbin are all considered part of the same species, then I think *Homo pekinensis* (Black & Zdansky 1927) (originally *Sinanthropus*) takes precedence?
You're not wrong. My feeling is that these should be considered as Homo sapiens. But for those who may be arguing for alternatives such as Homo longi or Homo juluensis, certainly Homo pekinensis has priority over those.
That just bumps the problem down to the subspecific epithet, doesn't it? *Homo sapiens pekinensis* or whatever.
It's interesting that in the morphology-based phylogenetic analyses done so far these come out outside the Denisovan–Neandertal–modern human clade, though. Not that morphology-based analyses have never turned out to be wrong....
Well, with morphology-based phylogenetic analyses, the recent work from Xijun Ni and others has been the only game in town lately, and there are quite a number of strange analytical decisions in that line of research (for instance, the linking of Harbin with mandibular specimens like Xiahe, despite them not sharing any characters at all).
If we look back more broadly, most morphological analysis since Weidenreich has emphasized sharing of characters between Zhoukoudian and other contemporaries in China with later Middle Pleistocene and Holocene people from the same region.
>China is the same story. Everything after around 600,000 years ago is Denisovan
But erectus still existed in SEA (though not China) until much later ~100 kya, right?
And also, presuming that erectus are the same as "superarchaics", where and when do you think their introgression into Denisovans occurred?
Big topic, but an important one!
Morphologically, it makes a lot of sense for later Indonesian samples like Ngandong to be southern Denisovans. Some of my work from 25 years ago focused on the morphological connections of Ngandong and early Australian skeletal samples. The finding of Denisovan ancestry in Papua and Australia makes this seem like a logical explanation. The Ngandong and Sambungmachan samples have substantially larger brain size than earlier Trinil-Sangiran samples, and a Middle Pleistocene introduction of a new Denisovan group might explain that.
Putting the Papuan-Philippines Denisovan ancestors into a geographic space is challenging if they are not Ngandong-like. If H. erectus was sitting on Java until 100,000 years ago, where were the Denisovans? It's hard to accommodate this problem with a double-dispersal after 100,000 years ago (Denisovans, then modern humans) because of the evidence for deep diversity in Indonesian Denisovans.
The reason to think that Ngandong is H. erectus and not Denisovan is the extent of shape similarity between this sample and the earlier Sangiran and Trinil material. Potentially that might be compatible with some superarchaic (=Sangiran erectus) contribution to the Indonesian Denisovan branch. Still, in the absence of DNA most assumed that there was a strong ancestry component in Ngandong from Sangiran. This is why Ngandong has been called H. erectus by so many people. But it is valuable to remember that they were seen as much more modern than Sangiran even at the time of their discovery.
Regarding the timing of superarchaic introgression, Rogers' most recent work still suggests a double contribution. The common ancestor of Neanderthal and Denisovan branches received close to 5% superarchaic, the Denisovans later received a smaller fraction, something like 2%. This model is also replicating the 2% Neanderthal-modern and 6% modern-Neanderthal fractions from other work, so I think it's tracking pretty well. The timing of the first pulse of superarchaic was then prior to 700,000 years ago. The Denisovan-specific superarchaic introgression is hard to date. So far all of the approaches for quantifying that introgression are relying on binning SNP counts and not linkage.
We would know more if we had better estimates of superarchaic fractions within the introgressed Denisovan components of living people. But it's admittedly a challenge to sort out the two Indonesian deep components. As far as I can remember, no one has looked hard at those Indonesian components to ask whether the appearance of two deep branches might instead be some superarchaic-mixed signal.
Thank you for such a comprehensive reply!
>later Indonesian samples like Ngandong to be southern Denisovans
I think it makes a perfect sense. It looks now that Denisovans were present and much diversified in Asia for a very long time, and it is very likely they swamped Erectus completely long ago, except maybe for small refugia islands like Flores.
I recall also an article by Wolpoff (your former advisor?) regarding continuity between Australia (Willandra lake) and SEA erectoid samples, which in light of what you wrote are likely of Denisovan lineage.
Interesting! There are some potential nomenclatural ramifications if this is true. If Zhoukoudian and Denisova and Harbin are all considered part of the same species, then I think *Homo pekinensis* (Black & Zdansky 1927) (originally *Sinanthropus*) takes precedence?
You're not wrong. My feeling is that these should be considered as Homo sapiens. But for those who may be arguing for alternatives such as Homo longi or Homo juluensis, certainly Homo pekinensis has priority over those.
That just bumps the problem down to the subspecific epithet, doesn't it? *Homo sapiens pekinensis* or whatever.
It's interesting that in the morphology-based phylogenetic analyses done so far these come out outside the Denisovan–Neandertal–modern human clade, though. Not that morphology-based analyses have never turned out to be wrong....
Well, with morphology-based phylogenetic analyses, the recent work from Xijun Ni and others has been the only game in town lately, and there are quite a number of strange analytical decisions in that line of research (for instance, the linking of Harbin with mandibular specimens like Xiahe, despite them not sharing any characters at all).
If we look back more broadly, most morphological analysis since Weidenreich has emphasized sharing of characters between Zhoukoudian and other contemporaries in China with later Middle Pleistocene and Holocene people from the same region.