The Human Family Tree, It Turns Out, Is Complicated

m.nautil.us/issue/102/hidden-truths/the-human-family-tree-it-turns-out-is-complicated

By Razib Khan June 30, 2021

We’re not the man we used to be. Over the last 20 years, genomics, ancient DNA, and
paleoanthropology have joined forces to completely overhaul our understanding of the
origin of our species. The true diversity and complexity of human evolution over the last
few hundred millennia surpasses even the most unhinged imaginings we might have
hazarded just a short generation ago. But greater clarity has left us with a messier and
less elegant narrative. Our species’ status, it turns out, is “complicated.”

In the year 2000, the orthodoxy was that humans spread across the world 60,000 years
ago, and were descended exclusively from a small population in Africa. Neanderthals and
various other human groups (and yes, we didn’t even deign to give them all names) were
evolutionary “dead ends.” Of interest mostly to scholars, they were dismissed as failed
experiments in a world our ancestors won. Today, this tidy story of us no longer passes a
basic fact check.

In 2010, genomes recovered from

ancient remains of “archaic
hominins” in Eurasia1 turned out to
have genetic matches in many
modern humans.2 It seems they
weren’t quite as “archaic” as we
thought. In addition, we had to get
used to the new reality that a solid
2 to 3 percent of the ancestry of all
humans outside Africa is
Neanderthal. About 5 percent of HUMAN BRANCHING: A stylized representation of
the ancestry of Melanesian groups, human lineages 50,000 years ago (excludes more distant
like the Papuans of New Guinea, ones, such as the “Hobbits” of Flores).Razib Khan
actually comes from a previously
unimagined new human lineage discovered in Denisova Cave, in Siberia of all places.

Since these first major overhauls, the genetic picture has only grown more complex.
Trace, but detectable (0.2 percent or so), levels of “Denisovan” ancestry are found across
South, Southeast, and East Asia (as well as among indigenous people of the Americas).3
Similarly, trace but detectable levels of Neanderthal ancestry actually appear in most
African populations.4 And, though we have no ancient genomes to make the triumphant
ID, a great deal of circumstantial DNA evidence indicates that many African groups
harbor silent “archaic” lineages equivalent to Neanderthals and Denisovans.5 We call
them “ghost” populations.6 We know they’re there in the genomes, but we have no fossils
to identify them with.

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Even the canonical “Out of Africa” migration7 itself has turned out to be less neat and tidy
than we thought. Outside Africa, whether you are an indigenous Australian, Amazonian
native or a German burgher, fully 90 to 99 percent of your ancestry derives from a single
ancestral human population pulse 60,000 years ago. Somehow, an isolated African tribe
of 1,000 to 10,000 people, who became genetically homogenous due to their initial small
population size, swept across Eurasia.8 By 50,000 years ago, they reached Australia.
They had replaced the last Neanderthals and Denisovans by 40,000 years ago, if not
earlier. They even migrated to North and South America 15,000 years ago.9

But inside of Africa, the story is much richer and still not fully grasped.10 Many African
populations started separating from each other 200,000 years ago, becoming distinct
lineages such as Khoisan and West Africans. The emergence of modern humans within
the continent was not an explosion, but a gradual evolution of interacting lineages. A slow
burn.11 The ancestors of modern non-Africans were part of this dance, but were isolated
at some point for tens of thousands of years, passing through the “great bottleneck.”
Where? When? Who knows? We can’t be sure at this point. Best to just come out and
admit it: This chapter of the story is still provisional.

It’s raining men

And now, one after another, new

dramatis personae, mostly ghosts,
keep entering stage left,
complicating what once seemed
our simple soliloquy. In The New
York Times, Carl Zimmer reports
on a very well-preserved fossil:
“Discovery of ‘Dragon Man’ Skull in
China May Add Species to Human “DRAGON MAN”: A nearly complete skull of Homo longi,
Family Tree.”12 Meanwhile, an an extinct species of archaic human, identified in Harbin,
Israeli group has a paper out in on the Northeast China Plain.Wikipedia
Science on a human population
discovered there which seems to resemble Neanderthals and dates to 120,000 to
140,000 years ago. “Dragon Man” is at least 140,000 years old, and it is a very well
preserved skull which exhibits a mixture of “primitive” and “modern” features.

Because these are brand new

finds, there is not yet consensus
about these fossils. Some
researchers want to call “Dragon
Man” Homo longi (pronounced
lóng, being Chinese for dragon), a
new human species, and assert its
features mean it is more closely IN THE FLESH: An illustration of what “Dragon Man”
related to modern humans than might have looked like.Wikipedia
Neanderthals.

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Paleoanthropologists outside of China seem more inclined to believe that “Dragon Man”
is actually the paradigm-busting species we have only known definitively from genomics:
Denisovans. This faction points out that “Dragon Man” had massive teeth, just like a
confirmed Denisovan jaw discovered in Tibet in 2019 (ancient-protein analysis indicated it
was Denisovan).13 So why do others disagree? Because the skull is so intact they
performed an evolutionary analysis of its relationships, using a full suite of characteristics
(unfortunately the find did not yield DNA). On that inferred family tree, Homo longi lies
closer to modern humans. In contrast, we know from genomics that Denisovans are more
closely related to Neanderthals than they are to modern humans.

My bet is that Homo longi and Denisovans are one and the same. Or, more precisely,
Homo longi is one of the many Denisovan lineages. Obviously, the researchers who did
the phylogenetic analysis know what they’re saying when they assert that this species
mixes modern and archaic features, but physical characteristics are less informative of a
lineage’s relationships than DNA is. There are several reasons for this. First, tens of
millions of variable markers in human genomes can be used as comparison points for
relationships.14 Physical characteristics are usually limited to hundreds of measurable
phenotypic traits (how many ways can you define skull shape or the size of teeth?).
Second, unlike assessed physical characteristics, DNA has zero subjective bias. A
genomic position is A, C, G or T. How many physical characteristics are you going to
define? How are you going to slice and dice skull shape? Modern imaging means that
these are objective measures, but humans still decide what to measure.

Finally, and more importantly,

physical characteristics are subject
to natural selection.15 Two
populations which look similar can
be quite genetically different
because adaptation drives
convergence, from different
starting points, toward similar
optimized external characteristics.
More concretely in this case, I
believe that Neanderthals adapted SKIN DEEP: The natives of the Andaman Islands, an
very well to the cold climate of archipelago in the northeastern Indian Ocean, are much
North Eurasia, and evolved away more genetically similar to a Swede than they are to any
African population.Wikipedia
from many ancestral human
characteristics that we now code
as “modern.”16 Yes, I’m saying modern humans are quite possibly more “primitive” than
our long-lost cousins. This Denisovan population and modern humans probably resemble
a general ancestral variety, while the Neanderthals were hyper-specialized in their
adaptations, an exemplar of evolution in overdrive.

What about the find in Israel? The discoverers of the Nesha Ramla Homo also want to
call it a new species, albeit one close to Neanderthals. But the fact of whether it is a new
species or not is mostly academic to me. What I find much more exciting is the fact that

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these people seem to be quite different from modern humans, but simultaneously have
tool technology that was undeniably quite advanced. From the remains at their sites,
Nesha Ramla Homo was a hunter of large and small game and maintained fires fueled by
wood. There were clearly cultural interactions between these humans and Africans to the
south, and Neanderthals to the north.

The “Out of Africa“ narrative of circa 2000 presented our own lineage as a superhuman
race, the apotheosis of human evolution. The telos of 2 million years of encephalization,
as human brains got bigger and bigger. The latest results do not fit easily into our old hero
narrative. Neanderthals win the contest for largest human brains. And “Dragon Man” turns
out to have had a very large brain too, in line with modern cranial capacities. All human
lineages were getting bigger-brained over the last few million years, not just the lineage
that led up to us.

The Denisovans were many

Finally, we need to acknowledge

that our long-standing and intimate
interest in Neanderthals may have
misled us when it came to
Denisovans. Neanderthals were
discovered in Europe, the
continent with the longest and
most well-funded tradition in
archaeology. But it turns out they HERE BE HUMANS: This cave, in the mountains of
may not be typical “archaic” Siberia, in Russia, has offered researchers a bounty of
humans. The best genetic work evidence about humanity’s deep past, including the
indicates that Denisovans were not discovery of the Denisovans. Both Neanderthals and
one homogeneous lineage, as evolutionarily modern humans are thought to have spent
time in the region near the cave simultaneously.Wikipedia
seems to have been the case with
Neanderthals, but a diverse group
that were strikingly differentiated.17 The Denisovan ancestry in modern populations varies
considerably in relatedness to the genome sequences from Denisova Cave. It is clear
that the Denisovan ancestry in Papuans is very different from the Siberian Denisovan
sequences. The most geographically distant Denisovan groups, those in Siberia and
those from on the far edge of Southeast Asia into Wallacea, were likely far more
genetically different from each other than Khoisan are from the rest of humanity.
Depending on the assumptions you set your “molecular clock” with, the most distant
Denisovan lineages probably separated into distinct populations from each other 200,000
to 400,000 years before their extinction.

Instead of thinking of three major human species 60,000 years ago, perhaps we need to
think of two families of related but heterogeneous populations (“modern humans” and
Denisovan humans) and one homogeneous one (Neanderthals). Denisovan humans
were clearly more closely related to Neanderthals than they were to modern humans.
Their common ancestors left Africa 600,000 to 750,000 years ago, and they separated
into western (Neanderthal) and eastern (Denisovan) branches. But the evolutionary

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history of Denisovans may share more commonalities with our African ancestors than
with their Neanderthal cousins, who occupied a much more constrained and forbidding
ecology across the northwestern ecozone of the continent. While the Pleistocene was
cold and brutal across the world, East Asia afforded more opportunities for Denisovans to
retreat southward into refuges than West Eurasia did for Neanderthals,18 which was
separated from African escapes by the Mediterranean and harsh deserts. Neanderthals
approached extinction several times for this reason, while Denisovans maintained many
different and diverse lineages down to the last 100,000 years.

But wait, there are more!

Neanderthals, Denisovans, and

modern humans are just the main
actors in the plotline of our
species’ recent origins. Today on
our planet there is just one human
species, but this is an exceptional
moment. For most of the past few
million years there were many
human species. Up until 50,000 A hobbit’s home: This cave, on the island of Flores,
years ago in the Southeast Asian Indonesia, held the remains of a potentially new human
islands of Flores and Luzon, we species, Homo floresiensis, discovered in 2003.Wikipedia
see strong evidence of very
specialized species of small humans, the pygmy Hobbits and Homo luzonensis. They are
different not only from each other, but from modern humans, Denisovans, and
Neanderthals. In Africa, there were almost certainly very different human populations
which over time were absorbed, just as the Denisovans and Neanderthals were. Homo
naledi in South Africa almost certainly persisted down to the period of the rise of modern
humans on the continent, 200,000 years ago.

Finally, a great deal of circumstantial archaeological and genetic evidence is

accumulating that some earlier African lineages related to modern humans expanded out
into eastern Eurasia before our own expansion. Artifacts in China19 and Sumatra20 dating
to before 60,000 years ago seem suspiciously modern, and genetic analysis of Siberian
Neanderthals dating to 120,000 years ago suggests admixture from populations related to
modern humans. It is still possible that Homo longi descends from one of these early
populations. Only DNA can establish this for a fact, but most older fossil remains do not
yield genetic material, and this skull is old enough that only perfect conditions would have
yielded DNA.

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Also in Evolution

Why It Pays to Play Around

By Andreas Wagner

The 19th-century physicist Hermann von Helmholtz compared his progress in solving a
problem to that of a mountain climber “compelled to retrace his steps because his
progress stopped.” A mountain climber, von Helmholtz said, “hits upon traces of a
fresh...READ MORE

The branches we pruned

Genetically, we’re a relatively homogeneous mammalian species, which underwent a

rapid expansion from a small ancestral population. This is particularly true outside of
Africa. All non-Africans share ancestry that dates back to a single tiny human population
of 1,000 to 10,000 people which flourished 60,000 years ago, and exploded across
Eurasia and Australia in a single sweep. Within Africa, there is more complex structure
and diversity than on the rest of the planet combined, but even there, many of the deep
differences are attributable to the great distinctness of the remnant hunter-gatherer
populations21: the Khoisan Bushmen, Hadza, and Pygmies of the rainforest. African
agriculturalists have undergone rapid expansions from small founding groups, though the
bottlenecks there were much less constrictive than for non-Africans.

Our planet was very different 100,000 years ago, and if we could survey that time, we
would be astounded by the human diversity across its surface. To enumerate what little
we know with certainty, there were at a minimum: modern humans, Neanderthals, at least
three to four varieties of Denisovans, and two pygmy Homo populations in Southeast
Asia. Likely there were still remnant Homo erectus in Southeast Asia as well, and other
diverged lineages within Africa, and a new Homo in Nesher Ramla, Israel, in the Middle
East with affinities to Neanderthals.

The first 20 years of this century have been the most exciting decades of
paleoanthropology since the emergence of the field, in large part due to the rise of
paleogenetics. I see no reason to assume that wave has crested. I for one, can’t wait to
continue constantly updating my priors on humankind as the 2020’s unfold.

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