Homo naledi genome: Will we ever find this elusive key to human evolution? – The Guardian

Homo naledi may have lived at the same time as the first modern humans. Left: Neo skull of Homo naledi. Right: Omo 2 skull, one of the earliest modern humans. Photo credit: Wits University/ John Hawks Photograph: Wits University

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 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 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 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 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 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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Homo naledi genome: Will we ever find this elusive key to human evolution? - The Guardian