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Homo naledi genome: Will we ever find

this elusive key to human evolution? |
Jennifer Raff | Science
Jennifer Raff
9-11 minutes

Despite what many people believe, paradigm-shifting moments in

science - where our understanding of a particular explanation is
challenged by a single finding - are actually quite rare. But one
happened in paleoanthropology on 9 May with the publication of
three linked papers describing new fossils belonging to the
enigmatic hominin Homo naledi.

Many people tend to think of human evolution as a very linear path:

from primitive creatures more or less directly to ourselves. But for
most of the history of evolution, there were multiple species of
hominins running (or climbing) around the African landscape, each
with their own unique physical adaptations to the challenges of
survival. As with all evolutionary experiments, some of these
adaptations proved more successful than others. Based on careful
study of fossils spanning millions of years in Africa,
paleoanthropologists thought they had a good understanding of how
the experiments results unfolded. Human evolution wasnt a straight
progression by any means, but more like a complicated bush, with
branches leading off in many directions. Still, there were definite

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trends that made their way into our textbooks. Hominin lineages with
some trait combinations died off without leaving any descendants. In
the lineages that persisted, brains got bigger, legs longer, arms
shorter, fingers less curved, teeth smaller.

It mostly made sense, and the new species discovered in a South

African cave in 2015 seemed initially to fit within this paradigm.
Homo naledi, as it was called, had some very primitive
morphological features that meant it was likely very ancient indeed -
possibly 2 million years ago, close to the root of our genus Homo.

But the recent discovery of a new set of H. naledi remains, in a

separate chamber of the same cave system, and the first direct
dates of the earlier H. naledi skeletons, has challenged this tidy
story. Shockingly, the remains dated to just 236-335,000 years ago.
This makes H. naledi very young: contemporaneous with early
modern H. sapiens elsewhere in Africa. Yet, as the new fossils
confirmed, H. naledi possessed a weird mosaic of primitive (ancient)
and derived (more human-like) traits, such as small brain sizes
(roughly a third of the size as ours: you can see the difference in the
picture above) but human-like hands and limbs.

One reason this has paleoanthropologists in an uproar is that it

means some features, such as small brain sizes, persisted long after
they thought it possible. Berger et al. suggests that in light of this,
we perhaps should be concerned about fossils which we have
assigned to species on the basis of morphology rather than direct
dates. If some remains have been misclassified, we may need to
change our ideas about how different hominin lineages evolved.
Another implication of these dates is that these hominins were
around South Africa when stone tools began to be made. While they
havent been found in association with any tools in the cave, we

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must still be open to the possibility that these small brained
hominins could have made them. Finally, whether or not the H.
naledi remains were deliberately buried inside the cave remains an
extremely contentious issue among paleoanthropologists. These
possibilities - both still unverified - pose a robust challenge for
archaeologists to grapple with.

Notably, there are some things that these fossils wont change: 1)
We are indeed the product of evolution (Im anticipating some of the
comments on this post inevitably challenging evolution. Sorry guys,
the evidence is incontrovertible and the fact that scientists change
their minds as to the details when new discoveries are made speaks
to the strength of the scientific process, not the weakness of the
theory). 2) Humans originated in Africa, 3) There were multiple kinds
of hominins co-existing for much of human evolution, 4) Humans are
likely descended from H. erectus, with subsequent ancestry from
some of the other kinds of hominins (Denisovans, Neanderthals,
and probably others).

So where does H. naledi fit within the overall picture of human

evolution in Africa? Its still unresolved. Berger et al. suggested
three scenarios: First, H. naledi belongs to one of the lineages
leading to H. habilis, H. rudolfensis, H. floresiensis, and A. sediba.
Alternatively, H. naledi is younger - a sister lineage to the clade that
contains H. erectus and the big-brained later hominins (including H.
sapiens). The final scenario is that H. naledi is even younger still - a
sister lineage to H. sapiens. Another possibility is that H. naledi is
the result of hybridisation between two or more lineages, perhaps
one related to humans and one related to Australopithecines.

The unusual combination of primitive and derived features of H.

naledi make distinguishing between the above scenarios difficult

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without genetic evidence. If we could get a genome from one or
more H. naledi individuals, we could determine the phylogenetic
relationship between it and the big-brained hominins: H. sapiens
and H. neanderthalensis (we dont yet know the brain size of
Denisovans). This would tell us whether or not human populations
had ancestry from this group (and perhaps others).

On a bioarchaeological level (assuming we could get DNA from

multiple individuals in the cave), we could ask whether H. naledi
individuals buried in the cave were close relatives, and whether
there was a relationship between burial location and genetic
relatedness. The answers to these questions might give us some
insights into the social structure of the species, whether the
individuals buried within the cave constituted a single population
close in time, or whether there is detectable genetic change over
time in the individuals within the cave. We could also use the
molecular clock to estimate the time of divergence of H. naledi to the
other hominins.

Ancient DNA could answer a lot of questions regarding H. naledis

ancestry and relationships, but unfortunately were not there yet.
While the dates of these fossils fit comfortably within the range at
which we can obtain ancient DNA (currently up to ~560780,000
years ago), Berger et al. notes in their paper that attempts to obtain
aDNA from H. naledi remains have thus far proven unsuccessful.
One of the team members, Dr John Hawks, noted on twitter in a
conversation with myself and others that three separate ancient DNA
labs have actually made the attempt without any luck (ours at the
University of Kansas wasnt one of them, for the record), but that
they will keep trying.

This is an important reminder of just how difficult and frustrating

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ancient DNA research can be, and if theres anything I wish the
interested public would know about it, its this: Behind the exciting
news that comes out every month about this ancient genome or that
lie scores of failed attempts, and the frustrated tears of many
graduate students.

Ancient DNA preservation depends on many different variables,

such as the temperature(s), UV radiation, and pH the remains have
been subjected to, the type of bone, tooth, or tissue being sampled,
and the amount of water, salinity, microbes, and oxygen present in
the depositional context. This is why some very ancient bones will
yield their genetic secrets, while ones just a few hundreds of years
old wont no matter how hard you try. Furthermore, morphological
preservation of bone doesnt always correspond with biomolecular
preservation, and we cant necessarily know in advance whether
DNA will be present in a skeleton before we attempt to recover it.
Thus ancient DNA researchers must always be mindful about
addressing important questions, be responsible about sampling
fossils, and not commit too many resources (particularly money and
time) to samples which wont work. Knowing when to stop working
on a sample that wont yield DNA is almost as important as
determining which samples to attempt in the first place.

Will we ever get a H. naledi genome? Based on the hints weve

gotten so far, the odds dont look great. Just as with H. floresiensis,
the other small-brained hominin that persisted until quite recently
(50,000 years ago), their position in our family tree looks to remain
unclear for a while - a lesson to us about how much we still have to
learn. But if I werent relentlessly optimistic, I wouldnt have lasted
long in the world of ancient DNA research. Perhaps it will just take a
little more time and luck. Weve certainly seen these two variables in

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abundance throughout the remarkable story of H. naledis discovery.

Berger et al. Homo naledi and Pleistocene hominin evolution in

subequatorial Africa. eLife 2017;6:e24234. DOI: http://dx.doi.org
/10.7554/eLife.24234

Dirks PHGM et al. The age of Homo naledi and associated

sediments in the Rising Star Cave, South Africa. eLife
2017;6:e24231 DOI: http://dx.doi.org/10.7554/eLife.24231

Hawks J et al. New fossil remains of Homo naledi from the Lesedi
Chamber, South Africa. eLife 2017;6:e24232. DOI: http://dx.doi.org
/10.7554/eLife.24232

Thompson JC. Human evolution: New opportunities rising. eLife

2017;6:e26775 DOI: http://dx.doi.org/10.7554/eLife.26775

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