Author : Wahid Ahmad
Scientists
believe we separated from our closest relatives—chimpanzees and bonobos—over 6
million years ago. But the species we call Homo sapiens is thought to have
first appeared in Africa between 300,000 and 200,000 years ago. Since then,
humans have spread all over the world.
About 2.8
million years ago, the first members of our genus Homo appeared in East Africa.
Homo habilis, one of the earliest species, lived from roughly 2.4 million years
ago to 1.4 million years ago and made simple “Oldowan” stone tools—small flakes
and choppers—for cutting and pounding animal carcasses and plant materials.
By about 2
million years ago, a descendant lineage gave rise to Homo erectus in Africa.
The oldest securely dated Homo erectus cranium from Drimolen, South Africa, is
about 2 million years ago, and by 1.8 million years ago these populations had
dispersed into Eurasia (for example, Dmanisi in Georgia at 1.85 million years
ago). Homo erectus showed a leap in brain size, fully modern body proportions, and
a more sophisticated Acheulean toolset, including large bifacial handaxes.
Over the next
million years, Homo erectus diversified regionally. African forms sometimes
called Homo ergaster persisted alongside Asian populations (Java Man and Peking
Man) well into the Middle Pleistocene. In Africa and Europe, populations
gradually evolved larger braincases and more rounded skulls, setting the stage
for a new form by about 600 thousand years ago.
That new
form, Homo heidelbergensis, is recognized in fossils dating between 600000 and
200000 years ago —most famously the Mauer jaw in Germany and the Kabwe cranium
in Zambia (500 to 300 thousand years ago)
Homo
heidelbergensis populations built simple shelters, used wooden and stone-tipped
spears for hunting, and show evidence of fire use after about 400000 years ago.
By about
400000 years ago, European Homo heidelbergensis gave rise to the Neanderthals,
while African Homo heidelbergensis lineages evolved into anatomically modern
Homo sapiens around 300000 years ago. The earliest widely accepted Homo sapiens
fossils—those from Jebel Irhoud, Morocco—are dated to 300000 years ago, pushing
back the origin of our species across much of Africa. Subsequent dispersals and
episodes of interbreeding with Neanderthals and Denisovans would further shape
the genetic tapestry of all later humans.
Using DNA
from people living today, scientists have learned a lot about recent human
history—how our ancestors spread across different continents, for example. But
we still don’t know much about what happened long before modern humans
appeared, during the earlier phases of the human lineage, especially in the
Pleistocene period, which lasted from about 2.5 million to 12,000 years ago.
This early history is important if we want to fully understand where we came
from.
One of the
biggest challenges is that ancient DNA from Africa older than Homo sapiens is
extremely rare or missing, because it doesn’t preserve well in hot climates. So
instead of ancient DNA, scientists try to look for clues in the DNA of people
living today.
The DNA of
modern humans still carries signals of population changes from the distant
past. One of the ways scientists study this is through something called the
Site Frequency Spectrum —a tool that looks at how common or rare different
mutations are in the DNA of a population. These patterns can tell us how big or
small populations were in the past and when they may have gone through big
changes, like sudden shrinkage or growth.
Recently,
scientists used advanced mathematical modeling on DNA from today’s populations
to figure out what likely happened in the past. They uncovered a shocking
chapter in our history—a time when the human population dropped to dangerously
low numbers. This research shows that our ancestors went through a major
population bottleneck in the past, reducing the number of breeding individuals
to just around a thousand. That’s an incredibly small number—so small it nearly
led to extinction.
They studied
change in population size over time by analysing patterns in modern DNA. It
doesn’t rely on ancient DNA, instead, it uses
The method
was applied to DNA from 10 African and 40 non-African populations, focusing on
parts of the genome that aren’t influenced much by natural selection or
sequencing errors.
The results
showed that this population crash lasted for more than 10000 years and wiped
out about 66 per cent of the genetic diversity that would’ve existed otherwise.
That loss still affects us today—it shaped the genetic makeup of all modern
humans. Interestingly, this bottleneck happened long before the famous
“out-of-Africa” migration.
This means African and non-African populations were
already starting to diverge, even though they all experienced this ancient
genetic squeeze.
During the Early to Middle Pleistocene transition,
a severe population bottleneck was detected in all 10 African populations
studied but not in any of the 40 non-African populations.
Even though the severe bottleneck wasn’t directly
detected in non-African genomes, it still affected their population history.
After the bottleneck, the average population size in non-African populations
was about 20,000, while it was about 27,000 in African agriculturalist
populations—a difference likely caused by the hidden impact of the ancient bottleneck
on non-African groups. Because African populations did not leave the continent,
their genetic lineages preserved clearer signals of this early bottleneck
event.
In a focused analysis of the Yoruba population in
Nigeria, it was shown that even a small sample of three individuals could
detect the bottleneck. However, in non-African populations, the signal was too
weak to detect using standard methods. Non-African populations also experienced
the same severe bottleneck between 921,000 and 785,000 years ago, with their
population shrinking to around 1,450 breeding individuals—similar to the
results from African populations. This confirms that the bottleneck was a
shared and critical event in early human history.
To understand the severe population bottleneck
better, researchers simulated a gradual population decline starting 1.5 million
years ago. The population histories predicted by FitCoal from this simulation
were different from the patterns seen in actual human genetic data, which
suggests that the real bottleneck was likely a sudden event rather than a slow
decline.
The bottleneck lasted about 117,000 years and
reduced the human population to roughly 1,280 individuals—comparable to current
endangered species. This sharp decline resulted in the loss of about 98.7% of
ancestral humans and caused a significant drop—about 65.85%—in today’s genetic
diversity. It's possible the population size during the bottleneck was even
smaller than estimated due to hidden subgroups and natural fluctuations, which
may have also raised the risk of inbreeding and extinction.
Around 930,000 years ago, there was a major drop in
human population size, likely caused by drastic climate changes during the
Early to Middle Pleistocene transition—also called the “0.9 million years ago
event.” During this time, glaciations became longer and harsher, ocean
temperatures dropped to their lowest, and droughts and wildlife changes spread
across Africa and Eurasia.
The Early to Middle Pleistocene Transition,
which occurred roughly between 1.2 million and 0.5 million years ago,
marks a profound shift in Earth's climate system. During this period, the
dominant pattern of glacial-interglacial cycles transformed significantly.
Initially, Earth's glacial cycles followed a relatively regular rhythm of about
41,000 years, largely influenced by variations in the Earth's axial tilt
(obliquity). However, as the Early to Middle Pleistocene Transition
progressed, this pattern gave way to more irregular and extended cycles
averaging 100,000 years in duration. This change, despite no major
alterations in orbital forcing, suggests the growing influence of internal
climate feedback mechanisms.
One of the most notable climatic changes during the
Early to Middle Pleistocene Transition was the increased intensity
and duration of glacial periods. Ice sheets, particularly in the Northern
Hemisphere, began to expand more extensively and persist for longer durations.
Glacials became much colder, with greater volumes of ice and significantly
lower sea levels. In contrast, interglacial periods, although warmer, were
relatively brief. This resulted in a higher amplitude of climate
fluctuations and a marked asymmetry in glacial cycles—slow accumulation
of ice followed by rapid melting events. The climatic system thus became more
extreme and less predictable than in the preceding period.
Several factors are believed to have driven these
changes. Although orbital variations continued to influence climate, they alone
do not explain the shift in periodicity. One key hypothesis involves the dynamics
of ice sheets: by the Early to Middle Pleistocene Transition,
repeated glaciations had eroded much of the soft regolith (loose soil and
sediment) under the ice, exposing bedrock. This made it easier for ice sheets
to grow thicker and remain stable for longer periods. In addition, atmospheric
carbon dioxide levels began to drop more significantly during glacials,
enhancing the Earth’s cooling and reducing the climate system’s resilience.
This marked a transition toward a climate system more heavily influenced by internal
feedbacks and threshold responses.
The Early to Middle
Pleistocene Transition also had wide-ranging environmental consequences
across different regions. In Africa, the climate became cooler and drier
during glacials, leading to the contraction of forests and expansion of
savannahs. These shifts are thought to have played a role in hominin
evolutionary pressures, encouraging dispersal, behavioral adaptation, and
technological development. In Europe and Asia, expanding glaciers and
cold-steppe environments reshaped ecosystems and migration patterns of both
humans and animals. Meanwhile, marine sediment records show increased
ice-rafted debris and stronger contrasts between glacial and interglacial ocean
temperatures, indicating broader disruptions in global climate and ocean
circulation.
During the Early to Middle
Pleistocene transition (about 1.2 to 0.8 Million years ago), Africa’s
climate shifted from relatively stable humid conditions to long dry spells
punctuated by abrupt wet phases. These fluctuations fragmented dense forests
into isolated wooded patches and expanded grasslands and savannas across much
of the continent, forcing hominins to navigate a highly heterogeneous
environment
Tectonic activity along the East
African Rift System continued to reshape the landscape during this interval. As
rifting intensified, new lakes and river valleys formed in graben basins, creating
corridors for animal and hominin movement but also isolating populations on
uplifted rift flanks. This dynamic interplay of extension, volcanism, and
subsidence controlled local hydrology and vegetation patterns, further driving
habitat fragmentation.
Animal communities responded to
these environmental changes by favoring open‑habitat specialists.
Forest‑adapted primates and other woodland species declined in many regions,
while grassland‑adapted herbivores—antelopes, zebras, and grazing bovids—became
more abundant. This faunal turnover, documented in sediment cores from Lake
Magadi, coincided with hominin adaptations such as increased mobility and
endurance running, enabling early humans like Homo erectus to exploit savanna
resources more effectively
Stone‑tool traditions persisted
and diversified across Africa during this period. The Acheulean handaxe
industry, which originated around 1.7 Million years ago, continued to
dominate but exhibited regional variations by 1 Million years ago:
toolkits included smaller, more
refined handaxes and occasional pointed implements, likely reflecting
innovations in butchery and woodworking. Sites such as Olorgesailie show this
mix of classic and modified Acheulean forms, suggesting both technological
conservatism and experimentation
Hominin
anatomy also evolved gradually toward larger braincases and more modern skull
shapes. Fossils dated toward the end of the transition display intermediate
features between Homo erectus and later
forms often grouped as Homo heidelbergensis. These anatomical intermediates
hint at a lineage leading toward Homo sapiens, setting the stage for the
emergence of archaic and then anatomically modern humans
Evidence for controlled
use of fire and regular shelter use becomes clear in this period. At Wonderwerk
Cave in South Africa, microstratigraphic analysis of sediments dated to 1 Million
years ago has revealed in‑situ burned bone and ashed plant remains,
demonstrating that early Acheulean hominins were using fire inside caves. Alongside
this, rock shelters across southern Africa show signs of repeated occupation,
suggesting that fire and natural caves were integral to hominin survival in
cooler or drier microclimates
This ancient population
bottleneck might explain why very few hominin fossils from Africa and Eurasia
exist from 950 to 650 thousand years ago. In Africa, only a handful of fossils
from this time have been found in places like Ethiopia and Algeria, and they
show similarities to Homo heidelbergensis. These fossils differ from Homo
antecessor found in Spain, and East Asian fossils from this period belong
to Homo erectus, which likely didn’t contribute to modern human
ancestry.
Interestingly, during
this bottleneck, two ancestral chromosomes are believed to have fused into what
is now human chromosome 2—around 900 to 740 thousand years ago. This period may
also mark a key speciation event that gave rise to the shared ancestors of
modern humans, Neanderthals, and Denisovans, whose divergence happened around
765 to 550 thousand years ago.
After the bottleneck
ended, the human population in Africa rapidly grew—about 20 times larger—around
813,000 years ago. The use of fire, with early evidence from Israel around
790,000 years ago, may have helped this recovery. Climate improvements might
have also played a role.
During this severe bottleneck the
human population was extremely small—just about 1,280 individuals—for roughly
117,000 years. However, many questions remain, like where these people lived,
how they survived such difficult conditions, and why the population stayed so
small for so long. More research is needed to better understand this crucial
period in human evolution.
In a new analysis, researchers
took a closer look at the claims and found a few problems. To dig
deeper, the researchers ran other population analysis tools to track population
changes to the same data they didn’t find any severe bottleneck.
So, what’s the bottom line for
all of us? This new analysis suggests that its claim about a human population
crash 1 million years ago might not hold up. It’s a reminder that in
science, exciting ideas still need to be carefully tested—and the simplest
answer is often the best.
If a population
bottleneck truly occurred 1 million years ago, we should see its genetic
signature in all human populations, including those outside Africa.
However, this signal is notably absent in non-African groups. The common
explanation—that non-African populations lost these signals due to genetic
drift after migrating out of Africa—does not hold up. Mathematical models show
that a bottleneck of that magnitude would have left a clear imprint across all
human DNA, making its absence in non-Africans a significant red flag.
Next, they looked at newer
research that suggests humans didn’t come from one single ancient population.
Instead, it looks like there were two or more human groups, living
separately for a long time, which eventually came together and mixed. One study
suggests these groups split around 1.5 million years ago, and came back
together about 300,000 years ago. One of those groups might have gone
through a bottleneck—but that’s not the same event.
Researchers have
detected a deep split in human ancestry around 1.5 million years ago,
which rejoined about 300,000 years ago, coinciding with the emergence of
anatomically modern humans.
The ancestral split
involved two major lineages, A and B. Lineage A ultimately contributed
about 80% of present-day human ancestry, undergoing a significant
bottleneck shortly after its formation. Lineage B contributed about 20%,
and this introgression is shared by all living humans. While most introgressed
material from lineage B seems to have been selected against, certain
segments—particularly those associated with neural development and
processing—appear to have been retained, suggesting adaptive value.
The findings stand in
contrast to earlier models, which also posited deep population structure but
suggested continuous gene flow between diverging lineages rather than
complete isolation followed by a later admixture. The new analysis supports a pulse
model, where A and B remained isolated after their divergence, rejoining
around 300 kya.
The evolutionary
implications are profound. The two lineages A and B could correspond to archaic
Homo species such as Homo erectus or Homo heidelbergensis. Homo erectus
appears in the fossil record from about 1.9 million to 0.8 million
years ago and was the first hominin to spread beyond Africa. Homo heidelbergensis
lived from roughly 600,000 to 300,000 years ago and is often seen as the
common ancestor of both modern humans and Neanderthals. It had a larger brain
(about 1,200 cm³) and a more vertical forehead than H. erectus. So
far, no ancient DNA from either species has been definitively tied to the A or
B genetic lineages, making a direct fossil–genome match still out of reach.
The sharp bottleneck in
lineage A may reflect a founder event linked to a migration or
ecological separation. These findings raise further questions about the direction
of gene flow between modern humans and Neanderthals or Denisovans and about
which ancestral lineage those archaic hominins were more closely related to.
Connecting these genomic insights to the fossil record remains a key challenge
in human evolutionary studies.