Rebecca Rogers Ackermann

Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern Africa with no genetic evidence reported so far. In this work, we describe the mass spectrometric sequencing of enamel peptides from four ~2 million–year-old dental specimens attributed morphologically to P. robustus from the site of Swartkrans in South Africa. The identification of AMELY-specific peptides enabled us to assign two specimens to male individuals, whereas semiquantitative mass spectrometric data analysis attributed the other two to females. A single amino acid polymorphism and the enamel-dentine junction shape variation indicated potential subgroups present within southern African Paranthropus . This study demonstrates how palaeoproteomics can help distinguish sexual dimorphism from other sources of variation in African Early Pleistocene hominins.

The story of the Taung Child discovery is almost legend in palaeoanthropology. In it, Raymond Dart acquires a block of calcified sediment, painstakingly removes the fossil skull from the matrix, and publishes his description of the new species Australopithecus africanus in the journal Nature 1 , only to be rebuffed by the international scientific community, but ultimately vindicated decades later following subsequent discoveries in Africa and the debunking of the Piltdown forgery 2-4. Dart is portrayed as prescient, and as elevating the importance of Africa in the narrative of human origins. 5 But is this a biased and simplified narrative? This history played out over a period marked by colonialism, racism, racial segregation, and, ultimately, the implementation of apartheid, making the history of human origins research intimately intertwined with the prevalent socio-political landscape. Viewed against this backdrop, and with a contemporary lens, the figure of Dart, and palaeoanthropology on the African continent more broadly, is more complex and worthy of reflection. In this special issue, published exactly 100 years after Dart's original publication, we bring together a group of African researchers and international collaborators to offer our perspective on the science, history, and legacy of palaeoanthropology in South Africa and beyond. We are particularly interested in exploring how the history of the discovery of early hominins in South Africa, as it played out in a colonial context, impacted the scientific field of palaeoanthropology. Did it promote or limit scientific enquiry? In what ways? What were its cultural effects, and how do they play out in our current context a century later? How might we work to decolonise the discipline and its narratives? Our decision to mark the Taung centenary by publishing this collection of articles in an open access South African journal, and to centre the voices of South African researchers, was a deliberate one. Too often, African palaeoanthropological heritage is the domain of international teams, with little meaningful collaboration from local African researchers-a phenomenon increasingly being recognised as "helicopter science". 6-8 The paucity of diverse Global South perspectives has done a disservice to the field, and has led to the perpetuation of colonial legacies and practices, while at the same time rendering much of what is going on invisible internationally, as it is not the lived experience of the researchers being centred. In this light, our goal is to celebrate the remarkable science that the discovery of A. africanus enabled, but also to probe disciplinary legacies viewed through a critical lens that challenges us to do science better.

The concepts of explorer, expedition, and the combination of the two into the myth of the explorer have been integral parts of Western mentality for more than 200 years. Here we briefly outline the colonial origins of these ideas, and use this crystallised understanding of the explorer myth to consider how African palaeoanthropology in the 20th century and up to the present continues to carry many of these biased, outdated overtones – some more overtly than others. We examine how Raymond Dart and the discovery of the Taung Child were situated and storied within this explorer narrative. We also expand on how these outdated concepts persist in determining which scientific approaches and outcomes are valued and which are not, which in turn has perpetuated extractive approaches to palaeoanthropology and the marginalisation of Indigenous scientists. This is especially notable in fieldwork practices which, to this day, embody the explorer myth’s deeply problematic colonial ideals of Western, masculine moral and cultural superiority. By understanding the mindset behind the discovery and reporting of Dart’s work on the Taung Child, we can better understand why it still holds such sway in palaeoanthropology today, and propose important practical and cultural disciplinary changes that will allow us to move beyond these colonial and masculine ideas in a manner that creates a more equitable future for all scholars.

This piece reflects on the importance of and focus on heads – especially the collecting of skulls and its impacts – in alpha taxonomy, biological anthropology, and Western science more broadly. We consider how the announcement and overall discovery story of the Taung Child revolutionised our understanding of hominin cranial evolution, but also fit within these skull-collecting objectives and contributed to the palaeoanthropological fixation on the skull. We contextualise this within the history of ‘physical’ anthropology in light of its initial goals in scientific racism, and consider how this process of skull collecting has become normalised in the discipline as a result of this history. As evidence for this, we quantify the possible effects of skull-collecting by collating available data on the number of skulls versus post-crania curated in a representative South African collection and compare the number of skulls versus post-cranial hominin fossils that form part of species hypodigms. We also explore how the ownership of skulls and ownership of narrative in the discipline have been intertwined throughout its history. Finally, we focus on how this early overemphasis on skulls, and especially brain size/intelligence, may have skewed our understanding of human evolution and contributed to ideas of human exceptionalism.

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus , a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa ^1,2 and the nature of intraspecific variation ^3–6 are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus , as previously suggested based on morphology alone ⁶ . Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase (www.facebase.org, https://doi.org/10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).

The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA (“NUMTs”). NUMTs are considered “mtDNA fossils” as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).