Post by Admin on Aug 12, 2020 7:12:16 GMT
DISCUSSION
This project began with a puzzle. We had argued in 2017 that Neanderthals and Denisovans separated early, that their neandersovan ancestors endured a bottleneck of population size, and that the postseparation Neanderthal population was large (12). That analysis omitted singleton site patterns. Mafessoni and Prüfer (13) pointed out that introducing singletons led to different results. In response, Rogers et al. (16) agreed, but also observed that the with-singleton analysis implied that the Denisovan fossil was only 4000 years old—a result that is plainly wrong. Furthermore, a residual analysis showed that neither of the models under discussion in 2017 fit the data very well (16). Something was apparently missing from both models—but what? The present paper provides an answer to that question.
Our results shed light on the early portion of the middle Pleistocene, about 600 ka ago, when large-brained hominins appear in the fossil record of Europe along with Acheulean stone tools. There is disagreement about how these early Europeans should be interpreted. Some see them as the common ancestors of modern humans and Neanderthals (28), others as an evolutionary dead end, later replaced by immigrants from Africa (29, 30), and others as early representatives of the Neanderthal lineage (6, 7). Our estimates are most consistent with the last of these views. They imply that by 600 ka ago, Neanderthals were already a distinct lineage, separate not only from the modern lineage but also from Denisovans.
These results resolve a discrepancy involving human fossils from Sima de los Huesos (SH). Those fossils had been dated to at least 350 ka ago and perhaps 400 to 500 ka ago (31). Genetic evidence showed that they were from a population ancestral to Neanderthals and therefore more recent than the separation of Neanderthals and Denisovans (9). However, genetic evidence also indicated that this split occurred about 381 ka ago [(2), table S12.2]. This was hard to reconcile with the estimated age of the SH fossils. To make matters worse, improved dating methods later showed that the SH fossils are even older, about 600 ka, and much older than the molecular date of the Neanderthal-Denisovan split (32). Our estimates resolve this conflict because they push the date of the split back well beyond the age of the SH fossils.
Our estimate of the Neanderthal-Denisovan separation time conflicts with 381 ka ago estimate discussed above (2, 13). This discrepancy results, in part, from differing calibrations of the molecular clock. Under our clock, the 381-ka date becomes 502 ka (12), but this is still far from our own 737-ka estimate. The remaining discrepancy may reflect differences in our models of history. Misspecified models often generate biased parameter estimates.
Our new results on Neanderthal population size differ from those we published in 2017 (12). At that time, we argued that the Neanderthal population was substantially larger than others had estimated. Our new estimates are more in line with those published by others (2, 11). The difference does not result from our new and more elaborate model because we get similar results from model α, which (as in our 2017 model) allows only one episode of gene flow (table S2). Instead, it was including the Vindija Neanderthal genome that made the difference. Without this genome, we still get a large estimate (NN1 ≈ 11,000), even using model αβγδ (table S3). This implies that the Neanderthals who contributed DNA to modern Europeans were more similar to the Vindija Neanderthal than to the Altai Neanderthal, as others have also shown (11).
Our results revise the date at which superarchaics separated from other humans. One previous estimate put this date between 0.9 and 1.4 Ma [(2), p. 47], which implied that superarchaics arrived well after the initial human dispersal into Eurasia around 1.9 Ma. This required a complex series of population movements between Africa and Eurasia [(33), pp. 66 to 71]. Our new estimates do not refute this reconstruction, but they do allow a simpler one, which involves only three expansions of humans from Africa into Eurasia: an expansion of early Homo at about 1.9 Ma ago, an expansion of neandersovans at about 700 ka ago, and an expansion of modern humans at about 50 ka ago.
Our results indicate that neandersovans interbred with superarchaics early in the middle Pleistocene, shortly after expanding into Eurasia. This is the earliest known admixture between hominin populations. Furthermore, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. According to our estimates, neandersovans and superarchaics had been separate for about 1.2 Ma. Later, when superarchaics exchanged genes with Denisovans, the two populations had been separate even longer. By comparison, the Neanderthals and Denisovans who interbred with modern humans had been separate less than 0.7 Ma.
It seems likely that superarchaics descend from the initial human settlement of Eurasia. As discussed above, the large effective size of the superarchaic population hints that it comprised at least two deeply divided subpopulations, of which one mixed with neandersovans and another with Denisovans. We suggest that around 700 ka ago, neandersovans expanded from Africa into Eurasia, endured a bottleneck of population size, interbred with indigenous Eurasians, largely replaced them, and separated into eastern and western subpopulations—Denisovans and Neanderthals. These same events unfolded once again around 50 ka ago as modern humans expanded out of Africa and into Eurasia, largely replacing the Neanderthals and Denisovans.
This project began with a puzzle. We had argued in 2017 that Neanderthals and Denisovans separated early, that their neandersovan ancestors endured a bottleneck of population size, and that the postseparation Neanderthal population was large (12). That analysis omitted singleton site patterns. Mafessoni and Prüfer (13) pointed out that introducing singletons led to different results. In response, Rogers et al. (16) agreed, but also observed that the with-singleton analysis implied that the Denisovan fossil was only 4000 years old—a result that is plainly wrong. Furthermore, a residual analysis showed that neither of the models under discussion in 2017 fit the data very well (16). Something was apparently missing from both models—but what? The present paper provides an answer to that question.
Our results shed light on the early portion of the middle Pleistocene, about 600 ka ago, when large-brained hominins appear in the fossil record of Europe along with Acheulean stone tools. There is disagreement about how these early Europeans should be interpreted. Some see them as the common ancestors of modern humans and Neanderthals (28), others as an evolutionary dead end, later replaced by immigrants from Africa (29, 30), and others as early representatives of the Neanderthal lineage (6, 7). Our estimates are most consistent with the last of these views. They imply that by 600 ka ago, Neanderthals were already a distinct lineage, separate not only from the modern lineage but also from Denisovans.
These results resolve a discrepancy involving human fossils from Sima de los Huesos (SH). Those fossils had been dated to at least 350 ka ago and perhaps 400 to 500 ka ago (31). Genetic evidence showed that they were from a population ancestral to Neanderthals and therefore more recent than the separation of Neanderthals and Denisovans (9). However, genetic evidence also indicated that this split occurred about 381 ka ago [(2), table S12.2]. This was hard to reconcile with the estimated age of the SH fossils. To make matters worse, improved dating methods later showed that the SH fossils are even older, about 600 ka, and much older than the molecular date of the Neanderthal-Denisovan split (32). Our estimates resolve this conflict because they push the date of the split back well beyond the age of the SH fossils.
Our estimate of the Neanderthal-Denisovan separation time conflicts with 381 ka ago estimate discussed above (2, 13). This discrepancy results, in part, from differing calibrations of the molecular clock. Under our clock, the 381-ka date becomes 502 ka (12), but this is still far from our own 737-ka estimate. The remaining discrepancy may reflect differences in our models of history. Misspecified models often generate biased parameter estimates.
Our new results on Neanderthal population size differ from those we published in 2017 (12). At that time, we argued that the Neanderthal population was substantially larger than others had estimated. Our new estimates are more in line with those published by others (2, 11). The difference does not result from our new and more elaborate model because we get similar results from model α, which (as in our 2017 model) allows only one episode of gene flow (table S2). Instead, it was including the Vindija Neanderthal genome that made the difference. Without this genome, we still get a large estimate (NN1 ≈ 11,000), even using model αβγδ (table S3). This implies that the Neanderthals who contributed DNA to modern Europeans were more similar to the Vindija Neanderthal than to the Altai Neanderthal, as others have also shown (11).
Our results revise the date at which superarchaics separated from other humans. One previous estimate put this date between 0.9 and 1.4 Ma [(2), p. 47], which implied that superarchaics arrived well after the initial human dispersal into Eurasia around 1.9 Ma. This required a complex series of population movements between Africa and Eurasia [(33), pp. 66 to 71]. Our new estimates do not refute this reconstruction, but they do allow a simpler one, which involves only three expansions of humans from Africa into Eurasia: an expansion of early Homo at about 1.9 Ma ago, an expansion of neandersovans at about 700 ka ago, and an expansion of modern humans at about 50 ka ago.
Our results indicate that neandersovans interbred with superarchaics early in the middle Pleistocene, shortly after expanding into Eurasia. This is the earliest known admixture between hominin populations. Furthermore, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. According to our estimates, neandersovans and superarchaics had been separate for about 1.2 Ma. Later, when superarchaics exchanged genes with Denisovans, the two populations had been separate even longer. By comparison, the Neanderthals and Denisovans who interbred with modern humans had been separate less than 0.7 Ma.
It seems likely that superarchaics descend from the initial human settlement of Eurasia. As discussed above, the large effective size of the superarchaic population hints that it comprised at least two deeply divided subpopulations, of which one mixed with neandersovans and another with Denisovans. We suggest that around 700 ka ago, neandersovans expanded from Africa into Eurasia, endured a bottleneck of population size, interbred with indigenous Eurasians, largely replaced them, and separated into eastern and western subpopulations—Denisovans and Neanderthals. These same events unfolded once again around 50 ka ago as modern humans expanded out of Africa and into Eurasia, largely replacing the Neanderthals and Denisovans.
