The Climate Driven Narrative Of The Prehistory of India

 

These maps are useful in shedding light on the prehistory of India. 

The Harappans

The Gangetic plain is predominantly in the temperate zone which has the highest population density in India and the most agriculturally oriented economy. 

This region had agriculture very early on, probably no later than 4000 BCE and possibly sooner, initially using Fertile Crescent Neolithic crops, via the Caucuses and Iran in its formative era, whose migrating farmers account for a significant share of the genetic roots of of the Indus Valley Civilization (a.k.a. the Harappan civilization a.k.a. the Meluhha). The Harappan civilization later adopted rice as a crop as well, via Austroasiatic migrants from Southeast Asia who gave rise to the Munda languages of India, ca. 2000 BCE.

We know from well dated residues on Harappan pots, by the way, that curry was a Harappan invention that predated the Indo-Aryans and the Munda people.

The prevailing view is that Harappan society was united politically, perhaps in a federation of city-states, and was largely free of war or fortifications, apart from some trade outposts on its frontiers, until it collapsed. It has relatively modern plumbing for the Bronze Age and its cities lack obviously palatial complexes, that one might associate with a more hierarchal society dominated by local kings who simply enriched themselves. 

Harappan society had its own script. The majority view is that this was a proto-script used for accounting and trade purposes, similar to the Vinca script in the Neolithic Balkans and the earliest Sumerian cuneiform inscriptions, but not a full fledged written language.

Harappans had trade connections to Sumeria, where they had a historically attested trade colony, and based on those records, know that the Harappans called themselves the Meluhha. 

Meluḫḫa or Melukhkha (Sumerian: 𒈨𒈛𒄩𒆠 Me-luḫ-ḫaKI) is the Sumerian name of a prominent trading partner of Sumer during the Middle Bronze Age. . . . most scholars associate it with the Indus Valley Civilisation. . . . Sumerian texts repeatedly refer to three important centers with which they traded: Magan, Dilmun, and Meluhha. The Sumerian location of Magan is now accepted to be the area currently encompassing the United Arab Emirates and Oman. Dilmun was a Persian Gulf civilization which traded with Mesopotamian civilizations. The current scholarly consensus is that Dilmun encompassed Bahrain, Failaka Island and the adjacent coast of Eastern Arabia in the Persian Gulf.

The Harappans also had trade (and possibly a sphere of influence) in the adjacent region of Central Asia known as the BMAC (for Bactria–Margiana Archaeological Complex a.k.a. Oxus culture).

The BMAC culture (ca. 2400 BCE to 1700 BCE with some dispute over the dates on each end of this range) was wedged between the Indo-European Andronovo culture (ca. 2000 BCE to 1150 BCE) and the terminal Harappan/Indo-Aryan transition Cemetery H (ca. 1900 BCE to 1300 BCE), and Painted Gray Ware (ca. 1300 BCE to 300 BCE) cultures. 

The BMAC would have fallen to Indo-European advances before the Indo-Aryans arrived in what remained of the Harappan region, and before the proto-Indo-Iranians arrived in Iran.

The Yaz culture, which had previously been part of the BMAC cultural region, was abruptly replace by an Indo-Iranian early Iron Age culture around 1500 BCE, and is a likely source of the Avestan language and what became the Zoroastrian religion associated with it. The Yaz culture persisted until it was absorbed by the Achaemenid Empire in the 300s BCE.

The Ghaggar-Hakra river f.k.a. the Saraswati River, which features prominently in the Rig Vedas, once coursed through what is now arid Indian steppe along the dashed orange route shown in the map above. Its now mostly dry bed is the home of many Harappan ruins.

But, the Saraswati River dried up around 2000 BCE, as part of a major climate event which made the region more arid that stretched, at a minimum from Egypt to India, and caused the Middle Bronze Age Late Harappan society to collapse.

As explained, for example, in Sujay Rao Mandavilli, "The Demise of the Dravidian, Vedic and Paramunda Indus Hypotheses: A brief explanation as to why these three Hypotheses are no longer tenable" SSRN (August 25, 2020) and the sources cited therein:

Dravidian languages, Sanskrit or Paramunda languages could not have been candidates for the [language of the] Indus Valley Civilization which flourished from 2600 BC to 1900 BC in the North-West of India and Pakistan.

If anything, the evidence that none of these three historical linguistic hypotheses can be supported by the evidence is stronger now than it was twenty-five years ago. 

Like the Paleo-European languages (of which the only survivor is Basque), the Harappan language can probably never be fully reconstructed, even if we can glean some knowledge of it from inscriptions in Harappan script, and from substrate influences in Sanskrit and related languages, and areal influences on the Munda languages.

The Indo-Aryans

The Indo-Aryans, who had wheeled chariots and domesticated horses, and were used to a more arid climate, rushed in to fill the political vacuum. They may have had some farming, or may have ruled subject societies of farmers, but were ancestrally herders.

The Indo-Aryans arrived from Central Asia, ca. 2000 BCE - 1500 BCE, bringing with them Sanskrit, that later diversified into the various Indo-European languages of South Asia. The language of the Indo-Aryans extinguished the Harappan language as anything but a substrate influence on Sanskrit.

Another branch of the same people at about the same time gave rise to the oldest Indo-Iranians and the Mittani Kingdom in Northeast Mesopotamia in mostly what is now Iran. 

We know that Indo-Aryans were the conquerors and not the conquered, because Indo-Aryan genes are more common in higher castes in India, and because these genes have origins (confirmed with ancient DNA) from outside the Indian sub-continent.

The religion of the Indo-Aryan migrants and the Harappan religion mutually influenced each other to produce the early Vedic religion, that would eventually give rise to modern Hinduism. But, given the differences between the Vedic religion and the religions that emerged in other places that the Indo-Europeans conquered, and the Rig Vedic references to things like the Saraswati river societies that were gone or almost gone by the time that the Indo-Aryans arrived, we know that the Indo-Aryan religious tradition and the Harappan religious tradition both influenced the fused religion that emerged from their fused culture.

Genetic evidence tells us that more than one wave of Indo-Aryan migration affected the area of India where Indo-Aryan languages are now spoken.

The Dravidians

The monsoon driven tropical region (in a medium blue on the first map), that makes up most of Southern India, didn't adopt agriculture until the South Indian Neolithic revolution, around 2500 BCE, had significant reliance upon crops domesticated in the African Sahel, and even then, wasn't as optimal for agriculture. The Fertile Crescent package of crops wasn't naturally suited to this climate region and it took many centuries for these crops, under the close guidance of early farmers, to adapt to this tropical monsoon driven climate.

The Dravidian language family probably has its roots in the South Indian Neolithic revolution, probably from one of the South Asian hunter-gatherer population that was one of the first to adopt agriculture, possibly with some linguistic influence from the Africans who brought the Sahel African crops that made this Neolithic Revolution possible.

While the Harappan society had trading posts at the fringe of what was Dravidian India at the time, mostly along the northwest coast of the Deccan peninsula, the Harappans almost surely did not speak a Dravidian language and had only thin trade ties with Dravidian society.

The first wave of Indo-Aryan migration reached the Dravidian society, leaving traces in genetic admixture found in lower amounts in almost everyone in India, even Dravidians. In this initial wave, the fused Vedic religion took hold (although the preference for vegetarianism found among the formerly Harappan regions did not), and all but a small core of this region probably experienced language shift, with their local Dravidian dialects going extinct. The Dravidian society on the eve of the Indo-Aryan arrival was not as technologically advanced as the Harappan one, but also may not have been in as advanced a state of collapse as the Harappan civilization. The climate event that impacted the Harappans so decisively, may not have affected their part of the Deccan peninsula so strongly. 

But in Southern India, the Indo-Aryans were spread thin, were in an eco-region less familiar to them, and less completely dominated the Dravidian society. The core region )probably within the region where Telugu is now spoken) that held out expanded and reconquered almost all of the former Dravidian territory, bringing its sole surviving Dravidian dialect with it (which is why the Dravidian language family seems much younger than one that stretches back to the South Indian Neolithic). But this reconquest never ended up replacing the Vedic religion that had replaced or absorbed its own religion (which may not have been as well-developed as the Harappan religion, and arose in an illiterate society). Unlike Northern India, which had multiple waves of Indo-Aryan migration, no later big wave of Indo-Aryan migration followed the Dravidian reconquest of Southern India.

The geographic range of the Dravidian languages prior to the arrival of the Indo-Aryans was probably wider than it is today, possibly extending to the fringes of the Indus River Valley civilization, as indicated by toponyms in these regions.

But, the North Dravidian languages (Brahui in what is now Pakistan, and the Kurukh-Malto languages of Northeast India), were probably not part of the original Dravidian language range and were the product of much later colonizations (probably around 1000 CE in the case of Brahui, where it was spoken as a result of an elite driven language shift, similar to the one that occurred at about the same time in what is now Hungary, rather than a mass migration of Dravidians to the region). Oral traditions among the Krukh-Malto peoples, at least, assign their origins to Dravidian homelands further south.

Are Oxygen Levels Related To Earth's Magnetic Field?

The strength of Earth’s magnetic field seems to rise and fall in line with the abundance of oxygen in the planet’s atmosphere, a study of geological records spanning the past half a billion years has found.

From the journal Nature. 

Among other things, the overall oxygen levels in the atmosphere impacts how large animals get, with more oxygen favoring larger animals.

It isn't clear what causes drive the correlation, although there probably is a cause.

New World Y1K Demographic Trends

Viewing event 350 years apart as part of the same trend is further in the direction of lumping than I'm comfortable with, but it is good to have a perspective on the pre-Columbian Americas that isn't static, with the implicit assumption that it was always the way it was when Europeans first encountered it.

[A] team led by archaeologist Robert Kelly of the University of Wyoming has studied this period using a previously assembled database of some 100,000 radiocarbon dates from across the United States. (See “Save the Dates.”) They used the dates to track population movements and demographic decline during this turbulent era, which was marked by drought, warfare, and disease. “We knew in a piecemeal fashion that these conditions drove demographic changes in different regions,” says Kelly. “But the radiocarbon data gives us a powerful new tool to understand population decline across the continent.”

After dividing the United States into 18 watersheds, the team analyzed the frequency of radiocarbon dates in each region and demonstrated that a cascading demographic collapse began in the central Rockies around a.d. 800 and later accelerated in multiple regions of central North America after 1150. The team’s analysis shows that the population of watersheds in California, the Pacific Northwest, the Great Lakes, and New England actually grew during the same period. This was likely because groups made their way from regions stricken by drought and warfare toward the coasts. Nonetheless, the radiocarbon data suggests that the overall Native American population declined by at least 30 percent from its peak before 1150.

From Archaeology Magazine.

Early Homo Erectus In Spain And Where It Fits In The Larger Narrative

Overview

Anthropologists have found partial Homo erectus remains in Spain from 1.1-1.4 million years ago, adding to 1.97 million year old Homo erectus remains in Grăunceanu, Romania, and 1.77-1.85 million year old Homo erectus remains in Dmanisi, Georgia. 

Homo erectus first appears in Africa. Outside of Africa, Homo erectus remains are most often found in Indonesia and China, dating from around 108,000 years ago in Southeast Asia, back to about 70,000 years after this species evolved in Africa. 

Homo erectus went extinct in most of the world around 1,000,000 years ago, but persisted longer in Southeast Asia and possibly in East Asia, and relict populations of Homo erectus probably admixed with Denisovans at some point when both species existed. A major population bottleneck described below, probably took place in Homo erectus starting around 930,000 years ago, but it didn't result in the complete extinction of the species. Homo erectus was probably extinct by the time that modern humans first ventured beyond South Asia (not long after the Toba eruption ca. 75,000 years ago). It is plausible that the Toba eruption, followed by first contact with modern humans, may have led to the final extinction of Homo erectus, to the final extinction of H. floresiensis and H. luzonensis, and also to the extinction of Denisovans over most of their range (with the last relict Denisovans in Tibet probably going extinct in connection with their contacts with modern humans in this remote place).

We know that Homo erectus evolved in Africa rather than Eurasia, because that is where the species that Homo erectus evolved from, mostly likely H. habilis, but possibly some other African archaic hominin, was located at the time, and not just because the oldest Homo erectus remains are found there.

The oldest identified H. erectus specimen is a 2.04 million year old skull, DNH 143, from Drimolen, South Africa, coexisting with the australopithecine Paranthropus robustus. H. erectus dispersed out of Africa soon after evolution, the earliest recorded instances being H. e. georgicus 1.85 to 1.78 million years ago in Georgia and the Indonesian Mojokerto and Sangiran sites 1.8 to 1.6 million years ago.

(The quoted Wikipedia summary hasn't been updated to reflect the Romanian discovery announced earlier this year.)

Half a million years and a few hundred meters away from this site, there are Homo antecessor remains, from a time when Homo erectus had gone extinct in Europe, almost 700,000 years before Homo erectus went extinct in Asia.

The New Discovery

ATE7-1 fossil face (right) with mirrored 3D model (left). Credit: Maria D. Guillén / IPHES-CERCA / Elena Santos / CENIEH

When the global timeline passed one million years ago, more than half the span of hominin presence in Eurasia had already passed by. The earliest archaeological evidence in Eurasia is more than two million years old—found in places like Shangchen, China, and the Dawqara Formation of Jordan. Just this year Grăunceanu, Romania, joined the list of early archaeological traces of hominins in Europe, dating to an estimated 1.97 million years ago.

Still, I think about the threshold of one million years ago quite often. The number of sites in Eurasia with hominin evidence before one million years ago has grown quite large. It would have been hard to imagine this in 1990, when many scientists wondered if any sites in Eurasia were really older than this. Today there are many. And yet, the number of sites with fossils of hominins is quite a lot smaller than the number with stone artifacts or cutmarked animal bones. Most are in China or Indonesia, in addition to the exceptional site of Dmanisi, Georgia.

In western Europe there may be only two such sites, both in Spain: Sima del Elefante and Barranco Léon.

This week Rosa Huguet and collaborators have reported on a significant new addition to this very humble record. In work at Sima del Elefante in 2022, excavators uncovered a fragmentary facial skeleton, designated as ATE7-1. The estimated age of this fossil face is between 1.4 million and 1.1 million years ago. The new fossil joins two other hominin fossils from this cave deposit, within the same range of ages, a finger bone and a fragment of the front portion of a mandible with several worn teeth, ATE9-1. These fossils have been previously published, the mandible in 2008.

None of these fossils provide much to go on. Huguet and coworkers compared the facial anatomy of ATE7-1 with fossil faces attributed to Homo erectus from Dmanisi, Georgia, and Sangiran, Indonesia. They also compared the face to fossils from Gran Dolina, Spain, attributed to Homo antecessor. This site is located only a few hundred meters from Sima del Elefante but represents hominins and stone artifacts from around 780,000 years ago—as much as a half million years or more later than Sima del Elefante.

The ATE7-1 face is more like most H. erectus faces than either is like the later Gran Dolina fossils.

From John Hawks.

Context

Where does this discovery fit in the larger narrative of archaic hominin evolution?

Neanderthals, Denisovans, and modern humans (i.e. Homo sapiens) all share a Homo erectus ancestor and probably also at least one intermediate archaic hominin ancestor that evolved from Homo erectus.

The oldest archaeological evidence of modern humans, which is, order of magnitude consistent with age estimates for the most recent common ancestor of all modern human uniparental Y-DNA and mtDNA lineages, is about 300,000 years ago in Africa. Modern humans first left Africa around 125,000 to 100,000 years ago, and did so via the Middle East rather than Iberia. But the lion's share of non-African modern humans appear to be descended from a later wave of modern human expansion out of Africa about 50,000-74,000 years ago, with the lion's share of that wave closer to 50,000 years ago than 74,000 years ago. Neanderthal populations largely stalled this expansion into Europe until about 40,000 years ago. One or more of the hominin populations of Southeast Asia, and the jungles of Southeast Asia, probably stalled modern human expansion via the Southern route into Asia until around the time of the Toba eruption around 74,000 years ago (with the eruption possibly weakening these barriers and possibly also creating a reason for the modern humans of South Asia to expand to the Southeast).

The oldest Neanderthal remains are about 430,000 years old. Neanderthals were moribund by 40,000 years ago (with modern human Cro-Magnon people entering Europe around the same time that Neanderthals became extinct and overlapping with them for periods of a thousand or two thousand years or so in any one place), with the final relict population going extinct around 29,000 years ago. The leading explanations for Neanderthal extinction include a wave of volcanic eruptions, climate change, and the growing superiority of modern human hunter-gatherers due to their cultural evolution (e.g. stone technologies and the domestication of dogs) and/or genetic evolution. The range of Neanderthals extended from Northern Wales to the Middle East to South Asia and the Altai Mountains. There was significant Neanderthal admixture with modern humans, probably around 50,000-100,000 years ago (the latest estimates tend to favor a more recent date) in the vicinity of the Middle East or Iran (leaving a DNA legacy in all non-African modern humans), and there was also a more modern admixture with Altai Neanderthals (leaving a DNA legacy in Asian modern humans). Non-Africans today have up to 2% Neanderthal DNA, with Asians having a little more than Europeans, although ancient DNA from modern humans in ancient Eurasia, much closer to Neanderthal admixture sometimes have higher percentages of Neanderthal admixture. Neanderthals had bigger brains than modern humans, but also a more static material culture and less diverse range of hunting prey heavily concentrated around large megafauna (suggesting reduced brain plasticity and less ability to adapt culturally rather than genetically), with modern humans also relied on a wider array of smaller prey like rabbits, smaller birds, fish, and other seafood. At the time of first contact with modern humans, the effective population size of Neanderthals was about ten times smaller than the effective population size of modern human Cro-Magnons, and the effective Neanderthal effective population size ranged from about 3,000-12,000 throughout their existence and was fractured into multiple more or less isolated regional subpopulations.

Wikipedia says this about the extinction of Neanderthals:

The extinction of Neanderthals was part of the broader Late Pleistocene megafaunal extinction event. Neanderthals were replaced by modern humans, indicated by the near-complete replacement of Middle Palaeolithic Mousterian stone technology with modern human Upper Palaeolithic Aurignacian stone technology across Europe (the Middle-to-Upper Palaeolithic Transition) from 41,000 to 39,000 years ago. Iberian Neanderthals possibly persisted until about 35,000 years ago, modern human expansion perhaps impeded by the Ebro River. Neanderthals in Gibraltar may have survived as late as 28,000 years ago at Gorham's Cave. The dating of these late Iberian sites is contested.

Historically, the cause of extinction of Neanderthals and other archaic humans was viewed under an imperialistic guise, with the superior invading modern humans exterminating and replacing the inferior species.

When sapiens began to expand and spread, he eliminated the other contemporary races [including Neanderthals] just as the white man drove out the Australian aborigines and the North American Indians.

— Ernst Mayr, 1950

The assimilation of Neanderthal populations into modern human populations had long been hypothesised with supposed hybrid specimens, and was revitalised with the discovery of archaic human DNA in modern humans. Similarly, the Châtelperronian industry of central France and northern Spain may represent a culture of Neanderthals adopting modern human techniques, via acculturation. Other ambiguous transitional cultures include the Italian Uluzzian industry, and the Balkan Szeletian industry.

Aside from competition with modern humans, Neanderthal extinction has also been ascribed to their low population as well as the resulting mutational meltdown, making them less adaptable to major environmental changes (specifically Heinrich event 4) or new diseases.

The admixture between modern humans and Neanderthals went in both directions. And, some of the late archaeological tool cultures of Neanderthal, which coincide with the arrive of modern humans in Europe, may reflect the increased brain plasticity of hybrid Neanderthal-modern human individuals.

Denisovans (named after the cave in the Altai where the type remains were discovered) probably existed from at least 285,000 years ago to about 25,000 years ago, general in Asia to the east of the Neanderthal range from Altai and Tibet to Southeast Asia, and overlapping with the Neanderthal range in the Altai region. High altitude adaptation DNA admixed from Denisovans are found in Tibetans. Trace levels of Denisovan admixture are found in mainland Southeast Asia and East Asia, and in island Southeast Asia up to the Wallace Line. Modern humans with Australian aboriginal ancestry or Papuan ancestry or Filipino negrito ancestry have substantial Denisovan ancestry (up to 6%) in addition to their Neanderthal ancestry (up to 2%). Presumably, the Denisovan-modern human admixture whose legacies exist in Australian aborigines, Papuans, Filipino negritos, and mainland Southeast Asians and East Asians must have occurred around the time of first contact between the first wave of modern humans in Asia around 50,000 to 75,000 years ago, and was then greatly diluted by subsequent waves of modern human migration west of the Wallace line in Asia. Also, Denisovans presumably went extinct within a thousand or two thousand years or so of first contact with modern humans (which took place much later in Tibet than almost everywhere else).

The exact path from Homo erectus to modern humans, Neanderthals, and Denisovans (and possibly other now extinct archaic species derived from Homo erectus) is a matter of ongoing investigation and debate.

Denisovan mtDNA diverged from that of modern humans and Neanderthals about 1,313,500–779,300 years ago; whereas modern human and Neanderthal mtDNA diverged 618,000–321,200 years ago. Krause and colleagues then concluded that Denisovans were the descendants of an earlier migration of H. erectus out of Africa, completely distinct from modern humans and Neanderthals.

However, according to the nuclear DNA (nDNA) of Denisova 3—which had an unusual degree of DNA preservation with only low-level contamination—Denisovans and Neanderthals were more closely related to each other than they were to modern humans. Using the percent distance from human–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago. 

Using a mutation rate of 1×10^−9 or 0.5×10^−9 per base pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively. Using 1.1×10^−8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using 5×10^−10 nucleotide site per year, it is 616,000 years ago. Using the latter dates, the split had likely already occurred by the time hominins spread out across Europe. 

H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans. Due to the strong divergence in dental anatomy, they [i.e. Denisovans] may have split before characteristic Neanderthal dentition evolved about 300,000 years ago.

The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population, possibly a relict H. erectus or H. erectus-like population about 53,000 years ago. Alternatively, divergent mtDNA could have also resulted from the persistence of an ancient mtDNA lineage which only went extinct in modern humans and Neanderthals through genetic drift. Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced. The mtDNA sequence from the femur of a 400,000-year-old H. heidelbergensis from the Sima de los Huesos Cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to Denisovans, and the authors posited that this mtDNA represents an archaic sequence which was subsequently lost in Neanderthals due to replacement by a modern-human-related sequence.

The intermediate species that is the most recent common ancestor of Neanderthals, Denisovans, and modern humans probably arose not long after a genetic bottleneck which has been inferred from modern DNA. This genetic bottleneck probably occurred in the clade of H. erectus which is ancestral to modern humans. As one secondary source explaining this notes:

Between 930,000 and 813,000 years ago, something nearly ended humanity before it even began. A mysterious bottleneck reduced the human breeding population to just 1,280 individuals, pushing our ancestors to the brink of extinction for an astonishing 117,000 years. 

Scientists have long puzzled over a gap in the African and Eurasian fossil records, and now, a team of researchers may have found the answer. Using a groundbreaking method called FitCoal, they analyzed the genomes of 3,154 modern humans to reconstruct ancient population sizes. What they found was staggering. Nearly 99% of early humans vanished, likely due to extreme climate events such as glaciations, severe droughts, and the collapse of ecosystems.

The world was changing. Glaciation, extreme droughts, and collapsing ecosystems made survival nearly impossible. Food sources vanished, and so did most of our ancestors. Those who remained – just a tiny fraction of the original population – fought to endure in a harsh and unpredictable environment. 

But against all odds, they survived. And in doing so, they may have changed the course of human evolution forever. Scientists believe this bottleneck could have led to the merging of two ancestral chromosomes, forming what we now know as chromosome 2 – a key feature that separates modern humans from other primates.

Around 813,000 years ago, the climate began to shift. Our ancestors may have mastered fire, allowing them to cook food, stay warm, and fend off predators. Populations rebounded, and from that tiny group of survivors, the future of humanity was born. 

This discovery reshapes our understanding of human history, and raises new questions. Where did these survivors live? How did they overcome such extreme conditions? Did this struggle push human intelligence to evolve faster?

The paper that is the basis for this account is Wangjie Hu, et al., "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition" 381(6661) Science 979-984 (August 31, 2023). Its abstract materials state:

Editor’s summary 

Today, there are more than 8 billion human beings on the planet. We dominate Earth’s landscapes, and our activities are driving large numbers of other species to extinction. Had a researcher looked at the world sometime between 800,000 and 900,000 years ago, however, the picture would have been quite different. Hu et al. used a newly developed coalescent model to predict past human population sizes from more than 3000 present-day human genomes (see the Perspective by Ashton and Stringer). The model detected a reduction in the population size of our ancestors from about 100,000 to about 1000 individuals, which persisted for about 100,000 years. The decline appears to have coincided with both major climate change and subsequent speciation events. —Sacha Vignieri 

Abstract 

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

The proposed climate event was part of the Mid-Pleistocene Transition. Some key aspects of this, in places where Homo erectus reached, were as follows:

Europe

In Europe, the MPT was associated with the Epivillafranchian-Galerian transition and may have led to the local extinction of, among other taxa, Puma pardoides, Megantereon whitei, and Xenocyon lycaonoides. The prevalence of ungulates adapted for grazing increased in the Mediterranean region after the "0.9 Ma event". The northern North Sea Basin was first glaciated during the MPT. The increased intensity of transgressive-regressive cycles is recorded in northern Italy.

Asia

The cooling brought about by the MPT increased westerly aridity in the western Tarim Basin. East Asian Summer Monsoon (EASM) precipitation declined. Grasslands expanded across the North China Plain as forests contracted.

During the MPT, the Indian Summer Monsoon (ISM) decreased in strength. In the middle of the MPT, there was a sudden decrease in denitrification, likely due to increased solubility of oxygen during lengthened glacial periods. After the MPT, the Bay of Bengal experienced increased stratification as a result of the strengthening of the ISM, which resulted in increased riverine flux, inhibiting mixing and creating a shallow thermocline, with stratification being stronger during interstadials than stadials. Paradoxically, variability in Δδ18O in the Bay of Bengal between glacials and interglacials decreased following the MPT.

Africa

In Central Africa, detectable floral changes corresponding to glacial cycles were absent prior to the MPT. Following the MPT, a clear cyclicity became evident, with interglacials being characterised by warm and dry conditions while glacials were cool and humid.

According to one of the leading papers on the 0.9 Ma Event, closely associated with the Homo erectus genetic bottleneck:

The Early-Middle Pleistocene Transition (EMPT) (ca. 1.4–0.4 Ma) represents a fundamental transformation in the Earth's climate state, starting at 1.4 Ma with a progressive increase in the amplitude of climatic oscillations and the establishment of strong asymmetry in global ice volume cycles. The progressive shift from a 41kyr–100kyr orbital rhythm was followed by the first major build-up of global ice volume during MIS 24-22, the so-called “0.9 Ma event”. The Vallparadís Section (Vallès-Penedès Basin, NE Iberian Peninsula) is one of the few Pleistocene series in Europe that spans the onset of the transition (from 1.2 to 0.6 Ma), thus representing a pivotal array of localities to investigate the effect of glacial dynamics on environmental conditions in Southern Europe. Here we inspect the effects of the EMPT on terrestrial ecosystems by examining the dietary adaptations (through dental meso- and microwear patterns) of fossil ungulates from the Vallparadís Section dated before and after the “0.9 Ma event”. Results show a steady presence of open grasslands before MIS 22 and more humid conditions at MIS 21. Both before and after MIS 22, a consistent presence of ungulates with long-term patterns that point to a grazing or grass-rich mixed feeding behaviour is observed, while noticeably, short-term patterns point to increased seasonality right after the “0.9 Ma event” glacial period. This increment of seasonality may have had an important effect on the Mediterranean habitats leading to recurring changes in the quality of plant resources available to large herbivores, which in response periodically adopted more mixed feeding behaviours widening their dietary breadth to consume also sub-optimal food items during adverse seasons.

In particular, during this event, global ice volumes increased substantially, and the Northern Hemisphere experienced increased seasonality and aridity, and surface sea temperatures in the North Atlantic reached their lowest values during the EMPT at this time. Also, grasslands expanded across the North China Plain as forests contracted.

This hypothesis is model dependent, could be impacted by sources of systemic error, like the possible much later extinction of Homo erectus populations derived from the same source population, later hard genetic sweeps of Homo erectus source genes, the effective extinction of modern humans arising from other clades of Homo erectus at some much later time, a lack of consideration of Neanderthal or Denisovan genes in the analysis, and a complete lack of ancient Homo erectus genomes. 

Also, in understanding this narrative one has to recognize that genetics researchers call an "effective population" of 1,280 individuals could have involved a census population at any one time that was many times larger than that. And, this is still about five times as large as the effective population size of the founding population of the Americas, for example. So, the bottleneck wasn't quite as extreme as some popular accounts of it would imply.

But the oldest examples of the species Homo antecessor does first appear in Europe, shortly after this inferred bottleneck, and there are no Homo erectus remains in Europe during or after the time of this inferred bottleneck.

Homo antecessor (Latin "pioneer man") is an extinct species of archaic human recorded in the Spanish Sierra de Atapuerca, a productive archaeological site, from 1.2 to 0.8 million years ago during the Early Pleistocene. Populations of this species may have been present elsewhere in Western Europe, and were among the first to settle that region of the world, hence the name. The first fossils were found in the Gran Dolina cave in 1994, and the species was formally described in 1997 as the last common ancestor of modern humans and Neanderthals, supplanting the more conventional H. heidelbergensis in this position. H. antecessor has since been reinterpreted as an offshoot from the modern human line, although probably one branching off just before the modern human/Neanderthal split.

Despite being so ancient, the face is unexpectedly similar to that of modern humans rather than other archaic humans—namely in its overall flatness as well as the curving of the cheekbone as it merges into the upper jaw—although these elements are known only from a juvenile specimen. Brain volume could have been 1,000 cc (61 cu in) or more, but no intact braincase has been discovered. This is within the range of variation for modern humans. Stature estimates range from 162.3–186.8 cm (5 ft 4 in – 6 ft 2 in). H. antecessor may have been broad-chested and rather heavy, much like Neanderthals, although the limbs were proportionally long, a trait more frequent in tropical populations. The kneecaps are thin and have poorly developed tendon attachments. The feet indicate H. antecessor walked differently than modern humans.

H. antecessor was predominantly manufacturing simple pebble and flake stone tools out of quartz and chert, although they used a variety of materials. This industry has some similarities with the more complex Acheulean, an industry which is characteristic of contemporary African and later European sites. Groups may have been dispatching hunting parties, which mainly targeted deer in their savannah and mixed woodland environment. Many of the H. antecessor specimens were cannibalised, perhaps as a cultural practice. There is no evidence they were using fire, and they similarly only inhabited inland Iberia during warm periods, presumably retreating to the coast otherwise.

Meanwhile:

Homo heidelbergensis (also H. erectus heidelbergensis, H. sapiens heidelbergensis) is an extinct species or subspecies of archaic human which existed from around 600,000 to 300,000 years ago, during the Middle Pleistocene. Homo heidelbergensis was widely considered the most recent common ancestor of modern humans and Neanderthals, but this view has been increasingly disputed since the late 2010s.

In the Middle Pleistocene, brain size and height were comparable to modern humans. Like Neanderthals, H. heidelbergensis had a wide chest and robust frame.

Fire likely became an integral part of daily life after 400,000 years ago, and this roughly coincides with more permanent and widespread occupation of Europe (above 45°N), and the appearance of hafting technology to create spears. H. heidelbergensis may have been able to carry out coordinated hunting strategies, and consequently they seem to have had a higher consumption of meat.

It is debated whether or not to constrain H. heidelbergensis to only Europe or to also include African and Asian specimens, and this is further confounded by the type specimen (Mauer 1) being a jawbone, because jawbones feature few diagnostic traits and are generally missing among Middle Pleistocene specimens.

H. heidelbergensis was subsumed in 1950 as a subspecies of H. erectus but today it is more widely classified as its own species. H. heidelbergensis is regarded as a chronospecies, evolving from an African form of H. erectus (sometimes called H. ergaster).

At least three other archaic hominin species overlapped with hominins from the H. erectus era or later.

• Homo floresiensis – Extinct small human species found in Flores
• Homo luzonensis – Archaic human from Luzon, Philippines
• Homo naledi – South African archaic human species

H. floresiensis and H. luzonensis may have been regional variations of the same species and show similarities with each other. The most plausible theory of their phylogenetic position, in my view, is that both of them were sub-species of H. habilis, and may have left Africa, either independently, or together with either H. erectus, the Denisovan ancestor, or Denisovans themselves. H. floresiensis and Denisovans (and possibly the earliest modern humans to arrive there as well) may have co-existed on the island of Flores, Indonesia (which is past the Wallace line) at some point in  time. There are no remains of H. floresiensis, H. luzonensis, H. habilis, or any other archaic hominins before H. erectus disperses from Africa. 

H. naledi was a South African archaic hominin species that flourished from 335,000 to 226,000 years ago, that was probably not directly ancestral to modern humans or any other non-African archaic hominins, but would have co-existed in time (and possibly space) with the earliest modern humans in Africa.

A November 6, 2024 post at this blog recapped some other possible non-African archaic hominins who existed at the same time that modern humans did: 

Notably the remains of the Red Deer Cave People of China from 14,000 years ago (a few thousand years before the start of the Holocene era) are genetically modern humans and are not archaic hominins despite some of their seemingly archaic features. See also here.

I am also inclined to think that they may yet be a small relict population of small archaic hominins in a remote Indonesian jungle on the island of Sumatra and perhaps Flores as well, where these cryptids, called Orang Pendek, locally, have been attested but not definitively confirmed to still exist. I discuss this further at this post.

Homo floresiensis (discovered in 2003) are commonly known as "hobbits" and have been found on the island of Flores. Their phylogeny is disputed, but I find the theory that they are an asian branch of H. habilis to be most convincing. H. luzonesis (discovered in 2007) is similar and contemporaneous, but found further east in the Philippines and is supported by a less complete archaeological record. Both of these diminutive species are found in association with late Pleistocene tools and "oriental fauna".

Personally, being more of a lumper than a splitter, I'm inclined to see H. floresiensis and H. luzonesis as sub-species variations of the same species ("race" within that species to use some outdated terminology), and likewise to see H. longi, H. juluensis, and Denisovans as sub-species variations of the Denisovan species. The Hualongdong archaic hominin fossils ... could be a hybrid individual, perhaps a Neanderthal-Denisovan hybrid individual (something that has precedent in a Denisovan cave DNA sample).

Academic anthropologists, in contrast, tend to be splitters, in part, because it is cool and career advancing to discover and name your own archaic species, in part because the data is so fragmentary that grouping different fragmentary remains in a clade presumes relationships between the remains that aren't solidly proven, and in part, because it is easy to underestimate how much morphological diversity is possible within a single species if populations of it exposed to different environmental conditions.

H. longi a.ka. "dragon man" dates to an earlier time period (still contemporaneous with modern humans in Africa) in China and Manchuria, was discovered in 1933, and has been hypothesized to be a sister clade to Neanderthals, Denisovans, and modern humans, and a descendant of the pre-modern human hominin species H. antecessor due in part to basal archaic features in the skull.

H. juluensis (literally "big heads") is contemporaneous H. longi, and beyond that time frame into the time frame of H. floresiensis and was discovered from 1976-1979 in China and Tibet. The authors assign this specimen along with Xiahe and Penghu fossils, to the Denisovan species (a sister clade to Neanderthals and modern humans) based upon comparisons of their fossil teeth and rough geographic proximity. H. juluensis is found in association with early Paleolithic tools and remains of Paleoarctic fauna. But they have larger brain cases than H. longi. A previous suggestions of the link between H. longi and the Denisovan species are discussed here and here at this blog. At least one Denisovan tooth has been found in Laos dated to 131,000 years ago.

The article also discusses the Hualongdong archaic hominin fossils that "date to the late Middle Pleistocene (~300,000 years BP) and display a mosaic of characteristics that cannot be easily fitted into any one lineage," although they are closer to H. longi and H. juluensis. This individual could be a hybrid between these two subspecies, with H. erectus, or with a Neanderthal who was far east of his usual range.

Prior to 2021, H. longi and H. juluensis tended to be classified as H. erectus (remains of which start to appear at a much greater time depth in Asia) or as archaic modern humans.

The Narmada and Maba partial skulls, especially the latter, are suggestively associated with Neanderthals by the article.

These Asian archaic species also overlap in time with the Southern African archaic hominin clade H. naledi which is a sister clade to the modern human ancestors and to the common ancestor of modern humans, Neanderthals, and Denisovans, but is not actually among our ancestors. As I explained at the link, this species "is basically a story from The Silmarillion of hominin evolution. It is entertaining, especially for hard core human evolution fans, but it doesn't really advance the plot."

A small number of papers reported genetic evidence in modern Africans of admixture with an archaic hominin "ghost species" in Africa, but subsequent papers have explained this "ghost species" signal as a methodological artifact that merely arises from population structure in early modern human Africans (see also here). But there may have been relict archaic hominins that did not admix with modern humans in Africa that were also contemporaneous with modern humans, at least, early on.

The question of whether behaviorally modern humans started showing advanced behavior around 70,000-50,000 years ago (at the dawn of the Upper Paleolithic era and close in time to the Out of Africa event for modern humans), was associated with an evolutionary leap in their brains is an open and unresolved question. See also here (addressing the question of what made modern humans genetically distinct from archaic hominins).

Quote Of The Day

Civilization exists by geologic consent, subject to change without notice.

—Historian Will Durant

Deep Genetic Modern Human Ancestry And Structure In Africa

A new paper at bioRxiv finds that:

The deep history of humans in Africa and the complex divergences and migrations among ancient human genetic lineages remain poorly understood and are the subject of ongoing debate. We produced 73 high-quality whole genome sequences from 14 Central and Southern African populations with diverse, well-documented, languages, subsistence strategies, and socio-cultural practices, and jointly analyze this novel data with 104 African and non-African previously-released whole genomes. We find vast genome-wide diversity and individual pairwise differentiation within and among African populations at continental, regional, and even local geographical scales, often uncorrelated with linguistic affiliations and cultural practices. 

We combine populations in 54 different ways and, for each population combination separately, we conduct extensive machine-learning Approximate Bayesian Computation inferences relying on genome-wide simulations of 48 competing evolutionary scenarios. We thus reconstruct jointly the tree-topologies and migration processes among ancient and recent lineages best explaining the diversity of extant genomic patterns. Our results show the necessity to explicitly consider the genomic diversity of African populations at a local scale, without merging population samples indiscriminately into larger a priori categories based on geography, subsistence-strategy, and/or linguistics criteria, in order to reconstruct the diverse evolutionary histories of our species. 

We find that, for all different combinations of Central and Southern African populations, a tree-like evolution with long periods of drift between short periods of unidirectional gene-flow among pairs of ancient or recent lineages best explain observed genomic patterns compared to recurring gene-flow processes among lineages. 

Moreover, we find that, for 25 combinations of populations, the lineage ancestral to extant Southern African Khoe-San populations diverged around 300,000 years ago from a lineage ancestral to Rainforest Hunter-Gatherers and neighboring agriculturalist populations. 

We also find that short periods of ancient or recent asymmetrical gene-flow among lineages often coincided with epochs of major cultural and ecological changes previously identified by paleo-climatologists and archaeologists in Sub-Saharan Africa.

Gwenna Breton, et al., "Ancient tree-topologies and gene-flow processes among human lineages in Africa" bioRxiv (July 16, 2024).

Thus, human evolution and genetic structure in Africa is not well-described by more or less random genetic exchanges between neighboring populations. Instead, massive, short, unidirectional introgression (i.e. one people conquering another) is the norm.

African and Arabian Paleoclimate

This paper leans heavily on Beyer, R.M. et al., "Climatic windows for human migration out of Africa in the past 300,000 years", 12(1) Nature Communications 4889 (2021) (open access), for its inferences based upon paleoclimate. Beyer (2021) concludes that:

there were a number of windows during the past 300k years when either northern or southern expansions out of Africa would have been climatically feasible. Prior to the last interglacial period, the Nile-Sinai-Land Bridge would have been crossable at several time intervals between 246k and 200k years ago. Following a reopening at 130k years ago, exits would have been intermittently possible until 96k years ago, and again later around 78k and 67k years ago. 

After that, this route likely remained closed until the wet Holocene. Provided that maritime travel was in principle possible, climatic conditions would have made southern exits feasible for a substantial proportion of the last 300k years. 

Before the last interglacial, there were three extended intervals of sufficient rainfall paired with relatively low sea level, from 275k to 242k years ago, from 230k to 221k years ago, and from 182k to 145k years ago. During most of the following window from 135k to 115k years ago, sea levels were particularly high, except at its beginning 135k years ago. This date is close to the proposed timing of an early northern exit; thus, if migration did occur, southern migrants might have encountered their northern counterparts on the Arabian Peninsula. Following a long period when the southern route was blocked, there was a sizeable window of sufficiently wet climate between 65k and 30k years ago. 

Further connections existed just after the Last Glacial Maximum, and during the mid-Holocene, consistent with evidence of Eurasian backflow into Africa. 

A threshold analogous to our estimate for precipitation exists for a Köppen aridity level around 1.7 based on the contemporary hunter-gatherer data, and the inferred periods of climatic connectivity between Africa and Eurasia are almost identical to those estimated for precipitation.

Our reconstructions suggest that there were several windows of suitable climate along either of the two possible dispersal routes that could have allowed the expansion of Homo sapiens out of Africa. 

Some of these windows predate the earliest remains outside of Africa, but are entirely compatible with genetic dating of introgression from Homo sapiens into Neanderthal, sometime between 250k and 130k years ago, and recent dating of material from Israel to possibly 194k years ago and from Greece to 210k years ago. 

Migrations into Eurasia were also likely feasible along both routes during the last interglacial period, when archaeological evidence points to a more sizeable exit. Two distinct scenarios for an exit around 65k years ago, the time that has been long suggested as the main moment of expansion out of the African continent based on archaeological and genetic evidence, are compatible with our estimates. This timing marks both the point shortly after which the northern route last was open before a period of 40k years of unsuitable climate, and the point at which the southern route first reopened for an extended period since the last interglacial period. 

The latter scenario has been a subject of debate based on the empirical palaeoenvironmental record, with conclusions ranging from the Arabian Peninsula being continually too arid for human migration, to intermittent wet intervals, and extended pluvial periods during marine isotope stage 3 (57–29k years ago). 

In any case, these inferences are not directly comparable with our results, both because several empirical proxies are not suitable for detecting rainfall of the small magnitude considered here (e.g. speleothems), and because, for each route, the specific path out of Africa that requires the least tolerance to low precipitation out of all possible paths varies over time, as does the geographic location of its driest segment; thus, our estimates would not be expected to necessarily display the same patterns over time as a localised empirical climate reconstruction. . . .

While archaeological and genetic data strongly suggest that Homo sapiens expanded its range towards Eurasia at least once prior to the large-scale colonisation wave beginning around 65k years ago, the reason for its initial failure to permanently settle outside Africa is less clear. 

Migration beyond the Arabian Peninsula would have been predicated on the ability to cross the Taurus-Zagros Mountain range while competing with Neanderthals in the north, which has previously been argued to have limited human expansions during the last interglacial period, and possibly other hominins, such as Denisovans (whose geographic range is unknown but likely covered a large portion of East Asia), in the east. 

In addition, our reconstructions suggest that climatically favourable intervals along both routes were frequently interrupted by periods of rainfall insufficient to support humans, which would have effectively isolated any of the earlier colonists that might have made it out of Africa. With a lack of demographic influx from further migration out of Africa, remnant populations on the Arabian Peninsula would have been susceptible to stochastic local extinctions driven by climatic fluctuations. 

This constraint would have been less important along the southern route during the unprecedentedly long period of largely favourable climate between 65k and 30k years ago, provided that maritime travel across a then 4 km wide strait of the Bab e-Mandeb made migration along this route possible. This long window would have provided ideal preconditions for a successful large-scale dispersal, allowing for a regular demographic influx from Africa that would have stabilised populations on the Arabian Peninsula, thus facilitating further expansion of Homo sapiens into Eurasia. 

These dynamics would have complemented technological, economic, social, and cognitive changes in human societies, which, possibly combined with the decline of Neanderthal, very probably accounted for the success of the late exit in the subsequent colonisation of Eurasia by Homo sapiens.

Khoisan Origins 

The Khoisan hunter gatherers of Africa have had distinct northern and southern subpopulations since roughly the time of genetic Out of Africa (ca. 50,000-80,000 years ago). This is a branch depth as deep as the divisions between Australian Aboriginal people and Swedish people in populations that live on opposite sides of the Kalahari desert in Southern Africa. The authors hypothesize that:

the global climatic shifts inducing massive ecological changes that have occurred in Africa at that time (e.g. (Beyer et al., 2021)), sometimes proposed to have triggered ancient Homo sapiens movements Out-of-Africa, may also have triggered, independently, the genetic isolation among ancestral Khoe-San populations. Nevertheless, where the ancestors of extant Khoe-San populations lived at that time remains unknown and is nevertheless crucial to further elaborate possible scenarios for the causes of the genetic divergence here inferred.

The common Khoisan ancestor population became distinct from other modern humans around 300,000 years ago, around the time that the modern human species emerged.

The Origins Of The Pygmies And Their Neighbors

Among Rainforest Hunter Gathers (RHG) in the Congo jungle, a.k.a. the Pygmies, there are genetically distinct populations in the West and in the East that date roughly to the Last Glacial Maximum (17,000 to 27,000 years ago). The authors explain that:

Rainforest Hunter-Gatherer populations across the Congo Basin diverged roughly between 17,000 and 27,000 years ago, relatively consistently across pairs of sampled populations used for inferences; estimates highly consistent with previous studies, despite major differences in gene-flow specifications across RHG groups between studies. Interestingly, this divergence time is relatively synchronic with absolute estimates for the Last-Glacial Maximum in Sub-Saharan Africa. The fragmentation of the rainforest massif during this period in the Congo Basin may have induced isolation between Eastern and Western RHG extant populations, as plausibly previously proposed. However, similarly as above for the Northern and Southern Khoe-San populations divergence, where the ancestors of extant Eastern and Western Rainforest Hunter-Gatherers lived remains unknown, which prevents us from formally testing this hypothesis.

This is around the time of the division between the founding population of the Americas and the populations of East Asia and Northeast Asia from which they originated. It is also a time frame during which Europe was depopulated except for relict populations in Iberia, the Italian Peninsula, and the Caucuses. 

The population ancestral to Rain Forest Hunter gathers and their agricultural neighbors branched between the neighboring population and the Rain Forest Hunter gatherer population, about 165,000 years ago. 

Key Short Duration Admixture Events In Africa

But, there were admixture events after that date. The authors explain that:

we found strong indications for almost synchronic events of introgressions having occurred during the Last Interglacial Maximum in Africa (Mazet et al., 2016), between ~90,000 and ~135,000 years ago (when considering 20 or 30 years per generation). They involved gene-flow between lineages ancestral to Khoe-San populations and ancestors of Rainforest Hunter-Gatherer neighbors on the one hand and, on the other hand, between lineages ancestral to Khoe-San populations and the lineage ancestral to all Rainforest Hunter-Gatherers. 

An increase in material-based culture diversification and innovation, possibly linked to climatic and environmental changes locally, has previously been observed during this period of the Middle Stone Age in diverse regions of continental Africa; prompting a long-standing debate as to its causes if human populations were subdivided and isolated biologically and culturally at the time[.] . . .

the instantaneous gene-flow event between the ancestral Rainforest Hunter-Gatherers lineage and that of their extant neighbors seemingly occurred synchronically to the genetic Out-of-Africa ((Beyer et al., 2021); see above). This would imply that possible climatic and ecological shifts at that time may not have only induced population divergences and displacement, but may also have triggered population gene-flow.

There was also a gene flow event between populations in Rain Forest Hunter Gather neighbors population, and the northern and southern Khoisan populations:

around 30,000 years ago, we found two loosely synchronic gene-flow events between ancestors to extant Central African Rainforest Hunter-Gatherer neighbors’ lineages and, separately, Northern and Southern Khoe-San lineages. This corresponds to the end of the Interglacial Maximum and a period of major cultural changes and innovations during the complex transition from Middle Stone Age to Late Stone Age in Central and Southern Africa. Nevertheless, connecting the two lines of genetic and archaeological evidence to conclude for increased population movements at the time and their possible causes should be considered with caution. Indeed, in addition to genetic-dating credibility-intervals being inherently much larger than archaeological dating, this period remains highly debated in paleoanthropology mainly due to the scarcity and complexity of the material-based culture records, and that of climatic and ecological changes locally, across vast regions going from the Congo Basin to the Cape of Good Hope.

And, there were also multiple gene flow events in the early Holocene era (roughly corresponding to the Neolithic era in Europe and into the European Copper/early Bronze Age):

we found strong signals for multiple instantaneous gene-flow events having occurred between almost all five recent Central and Southern African lineages between 6000 and 12,000 years ago, during the onset of the Holocene in that region, shortly before or during the beginning of the last Post Glacial Maximum climatic crisis in Western Central Africa, the emergence and spread of agricultural techniques, and the demic expansion of now-Bantu speaking populations from West Central Africa into the rest of Central and Southern Africa. These results are consistent with previous investigations that demonstrated the determining influence of Rainforest Hunter-Gatherer neighboring populations’ migrations through the Congo Basin in shaping complex socio-culturally determined admixture patterns, including admixture-related natural selection processes.

As our estimates for introgression events are in the upper bound of previous estimates for the onset of the so called “Bantu expansion” throughout Central and Southern Africa, we may hypothesize here that major climatic and ecological changes that have occurred at that time may have triggered increased population mobility and gene-flow events between previously isolated populations, rather than consider that the Bantu-expansions themselves were the cause for all the gene-flow events here identified.

Finally, we did not find signals of more recent introgression events from Bantu-speaking agriculturalists populations into Northern or Southern Khoe-San populations, in particular among the !Xun, albeit such events have been identified in several previous studies (see (Schlebusch and Jakobsson, 2018)). This is likely due to the fact that we considered only a limited number of individual samples from each population, and therefore may lack power to detect these very recent events with our data and approach.

Was There Archaic Admixture In Africa?

The new paper finds that it is possible to fit their data to a narrative without admixture with a ghost population of archaic hominins in Africa, as some studies have suggested, although that possibility is not ruled out either, and the authors of this study acknowledge that they are using fewer kinds of data to build their historical narratives than studies that found evidence of admixture with ghost archaic hominin populations in Africa.

Ragsdale and colleagues included in their models possible very ancient genetic structures, long before Homo sapiens emergence, a feature that is unspecified in our scenarios which considered simply a single ancestral population in which all extant lineages ultimately coalesce. Nevertheless, note that substructure and reticulation within the ancestral population is not per se incompatible with our scenarios. In fact, it may be compatible with our posterior estimates of a large effective population ancestral to all extant populations here investigated, the largest among all inferred ancient and recent Central and Southern African effective population sizes. . . . . 

We did not explore possible contributions from unsampled lineages, whether from non-Homo sapiens or from ancient “ghost” human populations, and therefore cannot formally evaluate the likeliness of the occurrence of such events to explain observed data. In all cases, our results demonstrate that explicitly considering ancient admixture from unsampled populations is not a necessity to explain satisfactorily large parts of the observed genomic diversity of extant Central and Southern African populations, consistently with a previous study (Ragsdale et al., 2023), and conversely to others (Lipson et al., 2022; Fan et al., 2023; Pfennig et al., 2023); at least when considering jointly the 337 relatively classical population genetics summary-statistics used here for demographic inferences. As discussed above, our results formally comparing competing-scenarios rather than comparing posterior likelihoods of highly complex yet vastly differing models, provide a clear and reasonable starting point for future complexification of scenarios comprising possible contributions from ancient or ghost unsampled populations, which will unquestionably benefit from the explicit use of additional novel summary statistics ((Ragsdale and Gravel, 2019; Fan et al., 2023; Ragsdale et al., 2023); see also above). 

In any case, the complexification of scenario-specifications to account for possible past “archaic” or “ancient” introgressions will not fundamentally solve the issue of the current lack of reliable ancient genomic data older than a few hundreds or thousands of years from Sub-Saharan Africa. Indeed, analogously to archaic admixture signals that were unambiguously identified outside Africa only when ancient DNA data were made available for Neanderthals and Denisovans (e.g. (Meyer et al., 2012; Prüfer et al., 2014)), we imperatively need to overcome this lack of empirical ancient DNA data in Africa to formally test whether, or not, ancient human or non-human now extinct lineages have contributed to shaping extant African diversity.

Side Observations Re Non-African Admixture

The study also made some side observations. For example, in its ancestry analysis at K=2 it effectively shows that amount of non-sub-Saharan African admixture present in various African populations. 

Unsurprisingly, this admixture is lowest in hunter-gather populations, modestly higher among non-hunter-gatherer Central and Southern Africans, higher still among the most northern East Africans, high among "Coloured" South Africans who have substantial non-African admixture, and predominantly non-African among North Africans.

Within non-Africans, Papuans pop out as a distinct population at K=5, and indigenous peoples of the Americas pop out as distinct at K=6.

Genetic Variation and Diversity

The paper also confirms conventional wisdom that African populations have more genetic diversity than non-Africans, even within sub-populations (and not merely because it is a large continent with many subpopulation that differ from each other). The amount of genetic variation in any subpopulation is strongly correlated with the amount of non-African admixture in a subpopulation (which less genetic variation associated with more non-African ancestry).

Weaknesses In The Paper

The most notable gap in the sample is a lack of DNA from Mozambique, whose people in Southeast Africa are known to be genetically quite distinct from other Africans, which local Bantu languages have click phonemes, presumably from a pre-Bantu substrate language.

The paper would also benefit from straying beyond its focus on the most basal populations of Africa to explore, at an at least superficial level, how this Central and Southern African population history fits into the larger global population of Homo sapiens.