Ancient DNA sheds new light on Neanderthal evolution
Genetic evidence suggests further migration to Europe 220,000 and 470,000 years ago
July 04, 2017
Ancient mitochondrial DNA from the femur of a Neanderthal helps to resolve the complicated relationship between modern humans and Neanderthals. The genetic data recovered by the research team, led by scientists from the Max Planck Institute for the Science of Human History and the University of Tübingen, provides a timeline for a proposed hominin migration out of Africa by a lineage more closely related to modern humans. These hominins interbred with Neanderthals already present in Europe, leaving their mark on the Neanderthals’ mitochondrial DNA. The study, published today in Nature Communications, pushes back the possible date of this event to between 470,000 and 220,000 years ago.
This femur of a Neanderthal provided evidence that ancestors may have included hominins from Africa who were closely related to modern humans.
Mitochondria are the energy-producing machinery of our cells. These mitochondria have their own DNA, which is separate from our nuclear DNA. Mitochondria are inherited from mother to child and can thus be used to trace maternal lineages and population split times. In fact, changes in the mitochondrial DNA can be used to distinguish groups and also to estimate the amount of time that has passed since two individuals shared a common ancestor, as these mutations occur at predictable rates.
Complicated relationship between Neanderthals and modern humans Prior research analyzing nuclear DNA from Neanderthals and modern humans estimated the split of the two groups at approximately 765,000 to 550,000 years ago. However, studies looking at mitochondrial DNA showed a much more recent split of around 400,000 years ago. Moreover, the mitochondrial DNA of Neanderthals is more similar to that of modern humans, and thus indicates a more recent common ancestor, than to that of their close nuclear relatives the Denisovans.
There has been debate about the cause of these discrepancies, and it has been proposed that a hominin migration out of Africa might have occurred prior to the major dispersal of modern humans. This human group, more closely related to modern humans than to Neanderthals, could have introduced their mitochondrial DNA to the Neanderthal population in Europe through genetic admixture, as well as contributing a small amount of nuclear DNA to Neanderthals but not to Denisovans.. However, more data was needed to evaluate the feasibility of this scenario and to define the temporal limits of the proposed event.
The femur of a Neanderthal excavated already in 1937 from the Hohlenstein-Stadel Cave close to Ulm provided just such an opportunity. “The bone, which shows evidence of being gnawed on by a large carnivore, provided mitochondrial genetic data that showed it belongs to the Neanderthal branch,” explains Cosimo Posth of the Max Planck Institute for the Science of Human History, lead author of the study. Traditional radiocarbon dating did not work to assess the age of the femur, which was instead estimated using the mutation rate as approximately 124,000 years old. This makes this Neanderthal specimen, designated HST by the researchers, among the oldest to have its mitochondrial DNA analyzed to date.
Interestingly, it represents a different mitochondrial lineage than the Neanderthals previously studied. Both lineages must have separated from each other very deeply in time, at a minimum of 220,000 years ago. The differences between their mitochondrial DNA indicate that there was more mitochondrial genetic diversity in the Neanderthal population than was previously thought. This suggests that the Neanderthal population size once was much bigger than that estimated for the final stage of their existence.
Timeline for additional migration of hominins out of Africa The proposed scenario is that after divergence of Neanderthals and modern humans (dated to a maximum of 470,000 years ago), but before the Neanderthals from Hohlenstein and the other Neanderthals diverged genetically (dated to a minimum of 220,000 years ago), a group of hominins moved from Africa to Europe, introducing their mitochondrial DNA to the Neanderthal population. Thus this intermediate migration out of Africa would have occurred between 470,000 and 220,000 years ago. “Despite the large interval, these dates provide a temporal window for possible hominin connectivity and interaction across the two continents in the past,” says Posth.
This influx of hominins would have been small enough that it did not result in a large impact on the Neanderthals’ nuclear DNA. However, it would have been large enough to completely replace the existing mitochondrial lineage of Neanderthals, more similar to the Denisovans, with a type more similar to modern humans.
"For a better assessment of the genomic relationships with Neanderthals, Denisovans and modern humans, nuclear data from the HST femur would be pivotal," Posth explains. It is extremely challenging, however, to retrieve nuclear DNA from the Neanderthal find from Hohlenstein due to poor preservation and high levels of modern human contamination. In any case, however, high quality nuclear genome data from more than one individual would be necessary to fully investigate this proposed wave of human migration out of Africa, and is an intriguing area for future study.
Nature Communications 8, Article number: 16046 (2017) doi:10.1038/ncomms16046 Received: 28 October 2016 Accepted: 23 May 2017 Published online: 04 July 2017
Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals
Cosimo Posth et al
Abstract Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.
Discussion
The African introgression hypothesis suggests that Late Pleistocene Neanderthal mtDNAs originated through gene flow from an African source8, which we constrain taking place more than ∼270 ka (Table 1). Our analytical calculations (Supplementary Table 8 and Supplementary Note 5) show that this event is plausible even if the introgressing lineage represented a minimal proportion of the initial gene pool. This scenario reconciles the discrepancy in the nDNA and mtDNA phylogenies of archaic hominins and the inconsistency of the modern human–Neanderthal population split time estimated from nDNA and mtDNA (Fig. 1d). Under this demographical model, the Denisovan mtDNA type was common among early Neanderthals in Eurasia (for example, Sima de los Huesos) and was then largely replaced by an introgressing African mtDNA that evolved into the Late Pleistocene Neanderthal mtDNA type. While the upper bound for the time of this putative gene flow event would be the divergence time between Neanderthal and modern human mtDNAs, here dated to 413 ka (95% HPD 468–360 ka), the lower temporal limit was represented so far by the ∼160 ka TMRCA of all published Neanderthal mtDNAs (Table 1). However, the finding of the deeply diverged HST lineage splitting from the Altai branch, ∼270 ka, sets an older lower boundary for the time of this admixture event. An alternative but less parsimonious scenario is that both HST and Altai mtDNA lineages reached Eurasia independently after diverging inside Africa. In that case the suggested introgression event might have occurred later but most likely before 160 ka, our estimated date for the start of the Altai branch diversification (Fig. 1c and Table 1).
The presence of modern human admixture into archaic humans has already been detected in the high coverage Neanderthal genome from the Altai region but not in sequences of chromosome 21 of two Neanderthals from Spain and Croatia14. The authors therefore suggested that a genomic contribution estimated between 0.1 and 2.1% occurred after the divergence of Altai from other late Neanderthals. However, there is a high level of uncertainty around the time of the inferred gene flow event since only one high coverage Neanderthal nuclear genome has been analysed so far. Moreover, the divergence time of the introgressing African population was estimated to date before or right after the TMRCA of modern-day humans (∼200 ka)14, while the mtDNA coalescence time between Neanderthals and modern humans is calculated at least twice as old (∼400 ka). The evolutionary scenario responsible for providing the mtDNA to the Late Pleistocene Neanderthals might have been an even earlier Middle Pleistocene gene flow from Africa, occurring in a time interval that we date between 413 and 268 ka (460–219 ka including upper and lower 95% HPD). It should be highlighted that this additional genomic contribution might have already been accounted for in ref. 14, which effectively measures the total amount of African introgression into Neanderthals after their split from Denisovans (473–381 ka; ref. 5).
The phylogenetic branch length of mtDNA sequences from 10 non-dated Neanderthal individuals was considered in BEAST, to assess individual molecular ages spanning from 130 to 40 ka. Although it is not known if the mtDNA mutation rate in modern humans is comparable to that of Neanderthals (Supplementary Note 4), molecular dating can at least be used to provide relative ages when the radiocarbon absolute chronometric method is not applicable. After the Altai mtDNA, HST is estimated to be the second oldest mtDNA with an age of 124 ka (95% HPD 183–62 ka). This wide temporal interval largely overlaps with the Marine Isotope Stage 5 (MIS 5: ∼130–73 ka)37. After its initial interglacial period (MIS 5e), central Europe was characterized by climatic fluctuations resulting in forestation cycles (MIS 5c/5a) alternated with the development of steppe-tundra biomass (MIS 5d/b)38. The stable isotopic δ13C and δ15N values of the archaic femur collagen and associated faunal remains support a more temperate, forested rather than a colder, steppe environment and is therefore consistent with an ecological context during the early warm phases of the last glaciation17.
Despite having only a single complete mtDNA on the HST lineage, the two highly differentiated Neanderthal mtDNA branches suggest higher mtDNA diversity during the Middle Pleistocene, which then declined during the Late Pleistocene (Supplementary Table 4). This observation is also supported by the steady decline in mtDNA effective population size displayed in the skyline plot before a steep growth in late Neanderthal population sizes (Supplementary Fig. 7). Studies focusing on the demographic patterns of late Neanderthals who overlapped with the earliest modern humans in Europe are of key importance to understand population dynamics and interactions between archaic and modern humans.
In conclusion, the HST mtDNA provided insights into the mtDNA diversity of Neanderthal populations through the Middle and Late Pleistocene. Its deep divergence time allowed us to further constrain the lower boundary for the time of the proposed African mtDNA gene flow into Neanderthal populations. The temporal corridor for this introgression event between 460 ka and 219 ka is compatible with the evidence of archaeological similarities between Africa and western Eurasia during the Lower to Middle Paleolithic transition39 and potentially may explain the dissimilarities in Middle Paleolithic industries between eastern and western Eurasia. Environmental changes across this time span might have facilitated a hominin expansion out of Africa and potentially spread cultural innovations such as the Levallois technology into Eurasia40. Alternatively, other scenarios such as multiple inventions of similar technologies by various hominin groups may explain the complex tapestry of technological variability during the late Middle Pleistocene.
Nuclear data from the HST femur would be pivotal in assessing its genomic relationships with Neanderthals, Denisovans and modern humans. However, the scarce preservation of HST endogenous DNA in combination with high level of modern human contamination challenge the retrieval of its complete genome. Analyses of high-quality nDNA from more than one well-preserved Neanderthal individual are necessary to detect the consequences of African admixture into archaic human populations.
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