It turns out that people today carry DNA inherited from Neandertals and other archaic humans, revealing that early H. sapiens mated with these other species and produced fertile offspring who were able to hand this genetic legacy down through thousands of generations. In addition to upsetting the conventional wisdom about our origins, the discoveries are driving new inquiries into how extensive the interbreeding was....
The study found that the Neandertal mtDNA sequences were distinct from those of contemporary humans and that there was no sign of interbreeding between them—a result that subsequent studies of mtDNA from additional Neandertal specimens confirmed.
Nobel scientist Svante Pääbo on Neanderthal genome retained at least 40% in modern humans
To many researchers, these ancient mtDNA findings put the nail in the coffin of the Multiregional Evolution and Assimilation models. Others, however, maintained that their reasoning suffered from a fundamental problem. The absence of a signal for interbreeding in any single independent region of the genome, such as in mtDNA, does not necessarily mean that other regions of the genome also lack signs of interbreeding.
The RRM2P4 and Xp21.1 evidence thus hinted that anatomically modern humans mated with archaic humans from Asia and Africa, respectively, rather than simply replacing them without interbreeding.
the greatest opportunity for interspecies coupling would have been in Africa, where anatomically modern humans and various archaic forms coexisted for much longer than they did anywhere else. Unfortunately, the tropical environments of the African rain forest do not favor the preservation of DNA in ancient remains.
We analyzed whole-genome sequence data from two contemporary Central African Pygmy hunter-gatherer populations and identified more than 250 genetic loci with strong archaic DNA signals. Our inferences provided evidence for more than a single mixing event between unidentified African archaic forms and anatomically modern Africans, with at least one such event occurring within the past 30,000 years.
We then searched a database of nearly 6,000 African Y chromosomes and identified 11 matches—all of which came from men who lived in a very small area of western Cameroon. Recently Fernando Mendez and his Stanford University collaborators reestimated the age of the time to the most recent common Y chromosome ancestor at 275,000 years, significantly older than the time of appearance of anatomically modern fossils in Africa. The presence of this very ancient lineage in contemporary people is a possible sign of interbreeding between H. sapiens and an unknown archaic species in western Central Africa.
in 2011, a group of paleontologists working at the Iwo Eleru site in Nigeria reanalyzed remains that exhibit cranial features intermediate between those of archaic and modern humans and determined that they date to just 13,000 years ago—long after anatomically modern H. sapiens had debuted. These results, along with similar findings from the Ishango site in the Democratic Republic of the Congo, suggest that the evolution of anatomical modernity in Africa may have been more complicated than any of the leading models for modern human origins have envisioned. Either archaic humans lived alongside modern ones in the recent past, or populations with both modern and archaic features interbred over millennia.
But given the current picture both inside and outside Africa, I favor models in which interbreeding was more common in the history of our species.
Given the complexity of the African fossil record, which indicates that a variety of transitional human groups, with a mosaic of archaic and modern features, lived over an extensive geographic area from Morocco to South Africa between roughly 200,000 and 35,000 years ago, I lean toward a model that involves interspecies mating during the archaic-to-modern transition. Sometimes called African Multiregional Evolution, this scenario allows for the possibility that some of the traits that make us anatomically modern were inherited from transitional forms before they went extinct.
Although archaic humans have often been seen as rivals of modern humans, scientists now must seriously consider the possibility that they were the secret of H. sapiens' success.
Michael F. Hammer - on Archaic human contributed to at least 5% of modern West African gene pool
Wow - in 2017 his research was shut-down? I emailed him asking him to reply publicly to this racist appropriation of his research!
https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(18)30117-4?&
We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones.
The oldest currently recognized members of the H. sapiens clade, from Jebel Irhoud in North Africa, have a facial morphology very similar to extant H. sapiens, as well as endocranial volumes that fall within the contemporary range of variation [2]. However, their braincase shapes are elongated rather than globular, suggesting that distinctive features of brain shape, and possibly brain function, evolved within H. sapiens [2, 5] (Figure 1). Other early H. sapiens fossils from Florisbad in South Africa (∼260 ka), Omo Kibish (∼195 ka) and Herto (∼160 ka), both in Ethiopia, are morphologically diverse [1, 16]. This diversity has led some researchers to propose that fossils such as Jebel Irhoud and Florisbad actually represent a more primitive species called ‘H. helmei’, using the binomen given to the Florisbad partial cranium in 1935 [17, 18]. In a similar vein, the fossil crania from Herto [19],
Available morphological, archaeological, genetic, and paleoenvironmental data indicate that the subdivision of Middle and Late Pleistocene African human populations drove the mosaic-like emergence and evolution of derived H. sapiens morphology. Reproductively semi-isolated populations adapted to local ecologies alongside drift.
Hammer replies to critique of his research
Among modern humans, the deepest-splitting branch is inferred to be the one leading to Central African hunter-gatherers, although four lineages diverge in a very short span: those contributing the primary ancestry to (a) Central African hunter-gatherers, (b) southern African hunter-gatherers, and (c) other modern human populations, along with (d) a “ghost” source contributing a minority of the ancestry in West Africans and the Mota individual. Central African hunter-gatherers separate into eastern (Mbuti) and western clades, with the latter then branching into components represented in Aka and Shum Laka. Next, a second cluster of divergences involves West Africans, two East African lineages (hunter-gatherer-associated and agro-pastoralist-associated), and non-Africans, the latter tentatively inferred to be a sister group to Mota but with no deep “ghost” ancestry. Within the West African clade, we identify Yoruba and Mende as sister groups, with Lemande as an outgroup, and most basally a separate West African-related lineage contributing to Shum Laka (64%). A Bantu-associated source (most closely related to Lemande) contributes 59% of the ancestry in Aka and 26% in Mbuti (who also harbor ancestry [17%] from an East African agro-pastoralist-related source). In a model separating the ∼8000 BP and ∼3000 BP Shum Laka pairs, the latter have ∼5% more Central African hunter-gatherer-related ancestry (as confirmed by the significantly positive statistic f4 (Shum Laka 8000 BP, Shum Laka 3000 BP; Yoruba, Aka) [Z=4.2]; Supplementary Information section 3).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386425/
Additionally, the adolescent male 2/SE II carried an A00 Y chromosome, suggesting that the concentration of this haplogroup in western Cameroon may have a long history, and moreover that A00 was formerly more diverse, given that the Shum Laka sequence falls outside of known present-day variation [12, 13]. The ∼300,000–200,000 BP divergence time of A00 from other modern human haplogroups [18, 19] could support its association either with the Central African hunter-gatherer-related ancestry component of the Shum Laka individuals or with the deep modern human portion of their West African-related ancestry.
Recent consensus has been that southern African hunter-gatherers, who split from other populations ∼250,000–200,000 BP, represent the deepest sampled branch of modern human variation [21, 24, 25]. Our results suggest that Central African hunter-gatherers split at close to the same time (perhaps slightly earlier), and thus that both clades, as well as the lineage that would later diversify at point (2), originated as part of a large-scale African radiation.
In addition to the well-characterized deep lineages, we also detect at least one deep “ghost” source contributing to West Africans and East African hunter-gatherers. This signal corroborates previous evidence for Hadza and Sandawe [39] and for West Africans [22], although we find that the best fit is a source splitting near the same point as southern and Central African hunter-gatherers.
The presence of deep ancestry in the West African clade is notable in light of the Pleistocene archaeological record [5, 40], which includes Homo sapiens fossils dated to ∼300,000 BP in northwestern Africa [41], as well as an individual with archaic features buried ∼12,000 BP in southwestern Nigeria (the oldest known human fossil from West Africa proper) [42
Based on our current understanding, the presence of at least four modern human lineages [West, South, Central (east/west) African] that diversified ∼250,000–200,000 BP and are represented in people living today supports archaeological evidence that this was a pivotal period for human evolution in Africa.
It turns out that people today carry DNA inherited from Neandertals and other archaic humans, revealing that early H. sapiens mated with these other species and produced fertile offspring who were able to hand this genetic legacy down through thousands of generations. In addition to upsetting the conventional wisdom about our origins, the discoveries are driving new inquiries into how extensive the interbreeding was....
The study found that the Neandertal mtDNA sequences were distinct from those of contemporary humans and that there was no sign of interbreeding between them—a result that subsequent studies of mtDNA from additional Neandertal specimens confirmed.
Nobel scientist Svante Pääbo on Neanderthal genome retained at least 40% in modern humans
To many researchers, these ancient mtDNA findings put the nail in the coffin of the Multiregional Evolution and Assimilation models. Others, however, maintained that their reasoning suffered from a fundamental problem. The absence of a signal for interbreeding in any single independent region of the genome, such as in mtDNA, does not necessarily mean that other regions of the genome also lack signs of interbreeding.
The RRM2P4 and Xp21.1 evidence thus hinted that anatomically modern humans mated with archaic humans from Asia and Africa, respectively, rather than simply replacing them without interbreeding.
the greatest opportunity for interspecies coupling would have been in Africa, where anatomically modern humans and various archaic forms coexisted for much longer than they did anywhere else. Unfortunately, the tropical environments of the African rain forest do not favor the preservation of DNA in ancient remains.
We analyzed whole-genome sequence data from two contemporary Central African Pygmy hunter-gatherer populations and identified more than 250 genetic loci with strong archaic DNA signals. Our inferences provided evidence for more than a single mixing event between unidentified African archaic forms and anatomically modern Africans, with at least one such event occurring within the past 30,000 years.
We then searched a database of nearly 6,000 African Y chromosomes and identified 11 matches—all of which came from men who lived in a very small area of western Cameroon. Recently Fernando Mendez and his Stanford University collaborators reestimated the age of the time to the most recent common Y chromosome ancestor at 275,000 years, significantly older than the time of appearance of anatomically modern fossils in Africa. The presence of this very ancient lineage in contemporary people is a possible sign of interbreeding between H. sapiens and an unknown archaic species in western Central Africa.
in 2011, a group of paleontologists working at the Iwo Eleru site in Nigeria reanalyzed remains that exhibit cranial features intermediate between those of archaic and modern humans and determined that they date to just 13,000 years ago—long after anatomically modern H. sapiens had debuted. These results, along with similar findings from the Ishango site in the Democratic Republic of the Congo, suggest that the evolution of anatomical modernity in Africa may have been more complicated than any of the leading models for modern human origins have envisioned. Either archaic humans lived alongside modern ones in the recent past, or populations with both modern and archaic features interbred over millennia.
But given the current picture both inside and outside Africa, I favor models in which interbreeding was more common in the history of our species.
Given the complexity of the African fossil record, which indicates that a variety of transitional human groups, with a mosaic of archaic and modern features, lived over an extensive geographic area from Morocco to South Africa between roughly 200,000 and 35,000 years ago, I lean toward a model that involves interspecies mating during the archaic-to-modern transition. Sometimes called African Multiregional Evolution, this scenario allows for the possibility that some of the traits that make us anatomically modern were inherited from transitional forms before they went extinct.
Although archaic humans have often been seen as rivals of modern humans, scientists now must seriously consider the possibility that they were the secret of H. sapiens' success.
Michael F. Hammer - on Archaic human contributed to at least 5% of modern West African gene pool
Wow - in 2017 his research was shut-down? I emailed him asking him to reply publicly to this racist appropriation of his research!
https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(18)30117-4?&
We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones.
The oldest currently recognized members of the H. sapiens clade, from Jebel Irhoud in North Africa, have a facial morphology very similar to extant H. sapiens, as well as endocranial volumes that fall within the contemporary range of variation [2]. However, their braincase shapes are elongated rather than globular, suggesting that distinctive features of brain shape, and possibly brain function, evolved within H. sapiens [2, 5] (Figure 1). Other early H. sapiens fossils from Florisbad in South Africa (∼260 ka), Omo Kibish (∼195 ka) and Herto (∼160 ka), both in Ethiopia, are morphologically diverse [1, 16]. This diversity has led some researchers to propose that fossils such as Jebel Irhoud and Florisbad actually represent a more primitive species called ‘H. helmei’, using the binomen given to the Florisbad partial cranium in 1935 [17, 18]. In a similar vein, the fossil crania from Herto [19],
Available morphological, archaeological, genetic, and paleoenvironmental data indicate that the subdivision of Middle and Late Pleistocene African human populations drove the mosaic-like emergence and evolution of derived H. sapiens morphology. Reproductively semi-isolated populations adapted to local ecologies alongside drift.
Hammer replies to critique of his research
Among modern humans, the deepest-splitting branch is inferred to be the one leading to Central African hunter-gatherers, although four lineages diverge in a very short span: those contributing the primary ancestry to (a) Central African hunter-gatherers, (b) southern African hunter-gatherers, and (c) other modern human populations, along with (d) a “ghost” source contributing a minority of the ancestry in West Africans and the Mota individual. Central African hunter-gatherers separate into eastern (Mbuti) and western clades, with the latter then branching into components represented in Aka and Shum Laka. Next, a second cluster of divergences involves West Africans, two East African lineages (hunter-gatherer-associated and agro-pastoralist-associated), and non-Africans, the latter tentatively inferred to be a sister group to Mota but with no deep “ghost” ancestry. Within the West African clade, we identify Yoruba and Mende as sister groups, with Lemande as an outgroup, and most basally a separate West African-related lineage contributing to Shum Laka (64%). A Bantu-associated source (most closely related to Lemande) contributes 59% of the ancestry in Aka and 26% in Mbuti (who also harbor ancestry [17%] from an East African agro-pastoralist-related source). In a model separating the ∼8000 BP and ∼3000 BP Shum Laka pairs, the latter have ∼5% more Central African hunter-gatherer-related ancestry (as confirmed by the significantly positive statistic f4 (Shum Laka 8000 BP, Shum Laka 3000 BP; Yoruba, Aka) [Z=4.2]; Supplementary Information section 3).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386425/
Additionally, the adolescent male 2/SE II carried an A00 Y chromosome, suggesting that the concentration of this haplogroup in western Cameroon may have a long history, and moreover that A00 was formerly more diverse, given that the Shum Laka sequence falls outside of known present-day variation [12, 13]. The ∼300,000–200,000 BP divergence time of A00 from other modern human haplogroups [18, 19] could support its association either with the Central African hunter-gatherer-related ancestry component of the Shum Laka individuals or with the deep modern human portion of their West African-related ancestry.
Recent consensus has been that southern African hunter-gatherers, who split from other populations ∼250,000–200,000 BP, represent the deepest sampled branch of modern human variation [21, 24, 25]. Our results suggest that Central African hunter-gatherers split at close to the same time (perhaps slightly earlier), and thus that both clades, as well as the lineage that would later diversify at point (2), originated as part of a large-scale African radiation.
In addition to the well-characterized deep lineages, we also detect at least one deep “ghost” source contributing to West Africans and East African hunter-gatherers. This signal corroborates previous evidence for Hadza and Sandawe [39] and for West Africans [22], although we find that the best fit is a source splitting near the same point as southern and Central African hunter-gatherers.
The presence of deep ancestry in the West African clade is notable in light of the Pleistocene archaeological record [5, 40], which includes Homo sapiens fossils dated to ∼300,000 BP in northwestern Africa [41], as well as an individual with archaic features buried ∼12,000 BP in southwestern Nigeria (the oldest known human fossil from West Africa proper) [42
Based on our current understanding, the presence of at least four modern human lineages [West, South, Central (east/west) African] that diversified ∼250,000–200,000 BP and are represented in people living today supports archaeological evidence that this was a pivotal period for human evolution in Africa.
https://www.science.org/doi/abs/10.1126/science.adh8140
Science, 5 Oct 2023
the RHG and San form a sister clade, deriving from a population ancestral to all other modern human populations. We find similar effective population sizes of the San and RHG from 50 to 200 kya (Figure 5), consistent with shared common ancestry.
. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from “ghost” populations with highly diverged genetic lineages.
in the recent past but at some time pre-dating the split of the two present-day populations, an unsampled “ghost” population splits from the ancestral population and at some point after this split but prior to the divergence of the two modern populations there is a pulse of gene flow from the ghost population into the population ancestral to the two modern populations
citing:
Recovering signals of ghost archaic introgression in African populations.
Sci. Adv. 2020;a handful of hominin fossils have been discovered at this site indicating human presence between 86 to 44 kyr. These fossils represent some of the oldest diagnosable H. sapiens craniomandibular remains in Southeast Asia. The TPL 6 frontal provides direct evidence of an early, possibly unsuccessful, dispersal from Africa or the Near East towards Southeast Asia by 70 ± 3 kyr.
https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.24915
Our work highlights the plurality of bone and stone toolmakers, in particular Paranthropus, H. habilis and H. erectus/ergaster for Oldowan assemblages. Similarly, in terms of anatomy, the type of dexterity required to make Oldowan assemblages is likely not limited to Homo genus. The frequency of Paranthropus remains associated with Oldowan assemblages is not negligible and insignificant. The occurrences between Oldowan assemblages and Paranthropus seem not to be coincidental and Paranthropus should be therefore considered as a stone and bone-tool maker in the same way as it is for early Homo.
https://www.sciencedirect.com/science/article/abs/pii/S0003552123000845
. Furthermore, the recent discovery of stone tools dated to 3.3 Ma in Kenya (LOM3 site) (evidence of stone-tools production, Harmand et al., 2015) and cutmarked bones at Dikika site dated to 3.4 Ma in Ethiopia (indicating stone-tool use, McPherron et al., 2010), is 300,000–500,000 years older than the earliest Oldowan technology (Braun et al., 2019, Plummer et al., 2023) and 500,000 years before the oldest known fossils attributed by some researchers to the Homo genus [Homo sp. remains at Ledi Geraru (Villmoare et al., 2015).
https://link.springer.com/chapter/10.1007/978-3-031-14157-7_15
The recent discovery of H. naledi confirms that at least one small-brained habiline-grade population survived until about 300,000 years ago.
Hominins moved between Africa and Europe several times, as indicated by the flow of genes and technology. The first Europeans appear to represent a primitive or transitional form of H. heidelbergensis. The species flourished later and overlapped with or evolved into the Neanderthals. The diversity observed among Middle Pleistocene Europeans may be partly explained by population collapse and repopulation during the Pleistocene glaciation cycles.
https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.24717
This new specimen extends the known brain size variability of Homo ergaster/erectus, while suggesting that differences in gross brain proportions among early human species, or even between early humans and australopiths, were absent or subtle.
https://www.elgaronline.com/monochap/book/9781035310005/book-part-9781035310005-9.xml
Natural selection first enlarged the sub-cortical areas of the brain where emotions are generated which, then, would allow the neo-cortex to grow since cognitions can only be remembered when tagged with emotions. Thus, increasing human emotionality was the force driving the evolution of the human brain. There are relatively few new structures in the human brain, compared to great apes (and hence the last common ancestor); most of the change increasing the size of brain structures, their connectivity, and some reorganization. There were roadblocks to hominin brain evolution, mostly caused by the problem of reworking the vocal tract to allow for speech. It took millions of years of natural selection working on vocalization eventually allowing for fine-tuned speech production. With speech came symbolic culture, and these new capacities fed back and allowed for continued growth of the sub-cortex and neo-cortex of humans to proportions current proportions.
Robin Dunbar:
Do Changes in Brain Volume Among Archaic Humans Reflect the Invention of Cooking?
- January 2023
Using thousands of unique 25 base pair sequences across the amylase locus, we showed that additional AMY1 gene copies existed in the genomes of four archaic hominin genomes, indicating that the initial duplication of this locus may have occurred as far back 800,000 years ago.
https://www.biorxiv.org/content/10.1101/2023.11.27.568916v3.abstract
Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy.
https://www.sciencedirect.com/science/article/abs/pii/S0047248414002644
In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production.
Received 21 February 2014, Accepted 28 October 2014, Available online 3 January 2015.
Our brains have evolved 23 times faster than other mammals, resulting in big brain sizes, the study published in journal Nature Ecology & Evolution states. Chris Venditti, the lead author of the study from the University of Reading, the United Kingdom, explained that the relationship between the brain and the body was assumed to be linear — meaning that brain size gets proportionally bigger the larger an animal is. The study, however, suggested there might be a physical limit to how large brains can become. “The brain is a fascinating organ — variation in its size has fundamental implications for intelligence, behaviour, sociality and ultimately, humanity,” Joanna Baker from the University of Reading and the co-author of the study, told Down To Earth.
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