In 2013 a large number of skeletons belonging to a previously unknown Hominin species were discovered in a newly discovered chamber within the Rising Star Cave System in the Cradle of Humankind at Maropeng, South Africa. This new chamber was named the Dinaledi Chamber (Chamber of the Stars in Sotho), and the new Hominin species was given the name Homo naledi ('naledi' meaning 'star'). A number of subsequent specimens assigned to the same species have been found in nearby chambers. Some of the specimens have been dated to between 335 000 and 236 000 years before the present, although it is possible that the total chronological range of all the specimens is longer.
Homo naledi is an unusual species, with a mosaic of modern and archaic traits. It has a small brain size, more comparable to that of an Australopithecene than an Archaic Human. The bones of the trunk and shoulders of Homo naledi also resemble those of Australopithecenes, yet the hands, lower limbs, and face of the species are far more Human.
A recent study of the teeth of Homo naledi found that they showed remarkably little variation, and concluded that this might indicate that all known specimens might belong to a single sex. However, estimating the sex of a specimen on bone-or-tooth morphology is a remarkably difficult process, particularly where there isn't a dimorphism (i.e. two consistently different forms) within the known specimens of that species.
Sex determination can also sometimes be achieved using ancient DNA recovered from specimens. However, DNA, while this has been used on some ancient Hominins from cool climates, DNA tends to degrade rapidly in warmer environments, such as South Africa.
In a paper published in the journal Cell on 24 June 2026, a team of scientists led by Palesa Madupe of the Globe Institute at the University of Copenhagen, the Human Evolution Research Institute at the University of Cape Town, and the Max Planck Institute for Evolutionary Anthropology, present the results of a study in which they assessed the sexes of all known specimens of Homo naledi using palaeoproteomic analysis of dental enamel.
The study focuses on amelogenins, a type of protein which helps to direct the mineralisation of tooth enamel. This the DNA which is used to make this protein is principally found on the X-chromosome, however, unlike many other genes, this has not been lost from the Y-chromosome, with the effect that there are two distinct forms of amelogenin, Amelogenin X, which drives from the version of the gene on the X-chromosome, and which is produced by all Humans, and Amelogenin Y, which is derived from the version of the gene on the Y-chromosome, and which is found only in males (albeit only making up about 10% of the total. This tool has previously been used to determine the sexes of other Pleistocene Hominins, making it a realistic choice for establishing the same in Homo naledi.
Madupe et al. began by taking surface etchings from four teeth, then processing them. All of the samples yielded the Amelogenin X variant, but none produced Amelogenin Y, indicating that all four were female. The samples were then subjected to a more destructive round of testing, crushing the teeth completely and then analysing the whole sample. This yielded identical results, indicating that the less destructive test was sufficiently reliable.
Following this success, Madupe et al. carried out an analysis of another nineteen Homo naledi teeth, using the non-destructive method (i.e. using surface etchings, not whole teeth). This included all 20 known Homo naledi specimens within the experiment. The Amelogenin X variant was again found in seventeen specimens, while the Amelogenin Y variant was again not detected. Two specimens yielded such low protein levels that they were excluded from the study, although these specimens also yeilded Amelogenin X variant at low levels and no Amelogenin Y variant. The Amelogenin Y variant was detected in all the controls used for the study, which comprised fifteen male Homo sapiens, two male Paranthropus robustus, a male Australopithecus africanus, a male Denisovan, and a male Homo antecessor.
The Amelogenin X protein found in Homo naledi showed no variation, something which would be considered extra-ordinary in a modern Human population, suggesting that either the species Homo naledi was remarkably genetically homogeneous, or that all of the individuals were very closely related. The individuals come from locations up to 145 m from one another within a complex cave system, and are not thought to have been deposited at the same time, making the former diagnosis more likely.
Madupe et al. identify eighteen confidently identified informative single amino acid polymorphisms on the Hominid Amelogenin X protein, two of which are notably different in Homo naledi and Modern Humans. One of these, a phenylalanine amino acid molecule at position 141 on the protein, is the same as that seen in present day Strepsirrhini (Lemurs, Galagos, Pottos, and Lorises) and Cercopithecidae (Old World Monkeys), but differs from the position in Modern Humans, Neanderthals, and Denisovans, all of which have a tyrosine amino acid at this point. The second, a proline amino acid at position 635, is the same character state as in all living non-Human Primates, but differs from the situation in Modern Humans, Neanderthals, and Denisovans, all of which have an alanine amino acid at this point. This location has not been recovered in any Homo antecessor, Homo erectus, or Australopithecus africanus specimen to date, but has been identified in two Paranthropus robustus specimens, both of which both had a proline amino acid in this position.
Analysis of the Amelogenin protein has previously been shown to be a useful way to identify the sex of a variety of Pliocene and Pleistocene Hominins. Application of this test to Homo naledi failed to identify any males among the 20 individuals currently known, nor any intra-specific variation on the protein, both highly unusual states. Notably, the study included individual UW 102a, popularly known as 'Neo' (pronounced ney-oh), the most complete Homo naledi specimen known, who has previously identified as male on the basis of a relatively robust skeleton (fortunately, the name Neo, which is Sotho and means 'gift', can be applied to either sex).
Since the method has previously been applied to individuals from South Africa as much as two million years old, and all of the male controls used within the study were identified as such, Madupe et al. do not believe there was anything wrong with the methodology being used. On this basis, they conclude that the Amelogenin Y variant was not present in any of the specimens, either because they were all female, or because of a mutation which prevented the expression of this protein in male Homo naledi. However, if the previous study on the dentition of Homo naledi is taken into account, it does raise the likelihood of all specimens being female.
Mutations which lead to the deletion or non-expression of the Amelogenin Y protein are known. They are more common in some Human populations than others (in one population in Pakistan, 8% of men did not produce this protein), and has been observed in a Neanderthal individual from Siberia. However, such mutations are typically extremely rare.
Since there is no reason to believe the sex ratio in living Homo naledi populations was anything other than 1:1, a random accumulation of 20 female specimens is incredibly unlikely. However, such a ratio is not inconsistent with the previously-made suggestion that the presence of Homo naledi specimens in the Rising Star Cave System may have been the result of deliberate mortuary practices rather than a random accumulation.
The Dinaledi Chamber is notoriously hard to access, to the extent that following its discovery, lead scientist Lee Berger assembled a team of physically small female palaeontologists and archaeologists with caving experience in order to carry our excavation work there. In theory, the cave could have been equally inaccessible to male Homo naledi, leading to a bias in the preservation of individuals there. However, ten of the known individuals are juveniles who died before their second molar erupted, an age at which it is unlikely that sex-related size-differences would have been sufficient to prevent males entering the site.
Exclusively female funerary sites are not known from any Modern Human population. The closest we have are the Neolithic Panoría site in Spain and Edcoural Cave site in Portugal, where females make up 70% and 67% of the population respectively, something which has been thought to reflect the greater importance of females in a matrilineal society. However, the Neolithic inhabitants of Iberia were still Modern Humans, very different to Homo neledi, a Pleistocene Hominin not interpreted to have been closely related to us, and the two groups cannot be expected to have had similar funerary practices (if Homo naledi indeed had these at all).
The expression of archaic amino acid variants in Homo naledi further supports the idea that this species was not closely related to Modern Humans, although the absence of data from archaic Homo species, such as Homo erectus or Homo antecessor, makes it hard to work out how distant a relationship this implies. Gathering such data for more Human and Australopithecene species may help to resolve the phylogentic position of Homo naledi. The less destructive sampling method used by Madupe et al. in this study should make such sampling easier that the earlier form of this technique, which required the destruction of whole teeth, a highly precious resource for extinct Hominins.
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