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Accurate diagnosis of bipolar disorder (BPD) is difficult in clinical practice, with an average delay between symptom onset and diagnosis of about 7 years. A depressive episode often precedes the first manic episode, making it difficult to distinguish BPD from unipolar major depressive disorder (MDD).
Aims
We use genome-wide association analyses (GWAS) to identify differential genetic factors and to develop predictors based on polygenic risk scores (PRS) that may aid early differential diagnosis.
Method
Based on individual genotypes from case–control cohorts of BPD and MDD shared through the Psychiatric Genomics Consortium, we compile case–case–control cohorts, applying a careful quality control procedure. In a resulting cohort of 51 149 individuals (15 532 BPD patients, 12 920 MDD patients and 22 697 controls), we perform a variety of GWAS and PRS analyses.
Results
Although our GWAS is not well powered to identify genome-wide significant loci, we find significant chip heritability and demonstrate the ability of the resulting PRS to distinguish BPD from MDD, including BPD cases with depressive onset (BPD-D). We replicate our PRS findings in an independent Danish cohort (iPSYCH 2015, N = 25 966). We observe strong genetic correlation between our case–case GWAS and that of case–control BPD.
Conclusions
We find that MDD and BPD, including BPD-D are genetically distinct. Our findings support that controls, MDD and BPD patients primarily lie on a continuum of genetic risk. Future studies with larger and richer samples will likely yield a better understanding of these findings and enable the development of better genetic predictors distinguishing BPD and, importantly, BPD-D from MDD.
Guided-jet waves have been shown to close resonance loops in a myriad of problems such as screech and impingement tones in jets. These discrete, upstream-travelling waves have long been identified in linear-stability models of jet flows, but in this work they are instead considered in the context of an acoustic-scattering problem. It is shown that the guided-jet mode results from total internal reflection and transmission of acoustic waves, arising from the shear layer behaving like a duct with some given wall impedance. After total reflection, only discrete streamwise wavenumbers may be supported by the flow, with these wavenumbers dictated by the fact that the standing wave formed inside of the jet must fit between the two shear layers. Close to the sonic line, the transmission of this mode to the outside is maximum, leading to a net-energy flux directed upstream, which dictates the direction of propagation of this mode, providing a clear connection to the better understood soft-duct mode (Towne et al., J. Fluid Mech., vol. 825, 2017, pp. 1113–1152). The model also indicates that these waves are generated in the core of the flow and can only be efficiently transmitted to the quiescent region under certain conditions, providing an explanation as to why screech is only observed at conditions where the discrete mode is supported by the flow. The present results explain, for the first time, the nature and characteristics of the guided-jet waves.
From the early second millennium AD more hierarchically organised societies marked by the rise of southern Africa’s first states developed in the north of southern Africa, culminating in Great Zimbabwe and its successors. This chapter outlines the processes involved, including the roles played by hunter-gatherer communities (for example at K2 and Mapungubwe) and the histories of farming societies on their periphery (notably those of Zimbabwe’s Nyanga Highlands). Much of this research is new and the past two decades have also seen challenges emerge to the importance previously accorded Indian Ocean trade in accounting for the emergence of social complexity, to the historical relationships between major centres (K2, Mapungubwe, Great Zimbabwe, Khami), and to understandings of the internal organisation, chronology, size, and functioning of those sites. Discussing these debates – particularly those relating to the settlement organisation of Great Zimbabwe and other stone-walled sites and the social implications of this – involves considering how far political action should be understood in terms of Indigenous, rather than Western, concepts.
This chapter begins by highlighting southern African archaeology’s importance at a global level, stressing the enormous time-depth over which hominins have been present in the region, the diversity of its archaeological record, and the contributions that this has made and continues to make to broader debates within archaeology and anthropology. Next, it indicates key changes made here relative to the first edition of this book in 2002 and then identifies the main sources of evidence available for reconstructing southern Africa’s past. These include archaeology, palaeoclimatic and palaeoenvironmental science, ethnographic data, historical linguistics, genetics, and oral and written histories. The chapter then introduces the overall structure of the book, ending with a discussion and justification of some key matters of nomenclature regarding how southern Africa’s varied inhabitants have been/should be called. Guidance is also given on matters of orthography relative to sounds not used in English.
Livestock first entered southern Africa a little over 2,000 years ago and by the mid−1600s Khoe-speaking herders were widely distributed across the western third of the region. Debates over how pastoralist societies developed and how and by what routes livestock were introduced have been transformed over the past two decades by significant major fieldwork projects, a growing number of detailed genetic and linguistic studies, and new interpretative frameworks partly inspired by deeper acquaintance with pastoralist practice in East Africa. Important advances have also been made in understanding Khoe rock art, the chronology of pottery, and the relevance of disease in constraining the southward spread of livestock. This chapter reviews these developments, while also grappling with the thorny question of how, if at all, forager and herder societies can be differentiated archaeologically and what form relations took between those who kept domestic livestock and those who did not. Questions of identity (ascribed and asserted) and the degree of coherence to be expected between genetic, linguistic, ethnographic, historical, and archaeological sources come to the fore.
Understanding the past requires understanding how it has been created. This is not simply about improving methodologies, but also the theoretical approaches employed and the broader socio-political framework within which they are applied. This chapter therefore delineates major developments in southern African archaeology from its nineteenth-century origins to the present, situating them with respect to the region’s wider history and the broader social and political context in which they emerged. It also considers how archaeological research was constrained by, but simultaneously challenged, structures of racial oppression during the twentieth century, differences in the experience of southern Africa’s states (including research disparities within and between them), some of the key paradigms within which archaeological research is currently conducted, and the problems encountered in making archaeology accessible to all sections of society. Another theme concerns the theoretical and methodological challenges that archaeologists face when invoking the ethnographies of southern Africa’s recent or contemporary inhabitants to help understand the past revealed by their research.
Only for the transition between the Pleistocene and the Holocene (c. 13,000−8,000 years ago) do we have a rich and chronologically relatively well-controlled record with which to explore the impacts on hunter-gatherer populations of the profound ecological changes associated with the shift from glacial to interglacial climates and through which to consider their own creativity at such a time. Previous archaeological work developed competing hypotheses to explain the shifts from microlithic to non-microlithic and back to microlithic (of a different kind) technologies during this period. These are considered here, along with potential evidence for patterns of social relations similar to those found in Bushman groups of the ethnographic present. At the same time, fuller publication of work from Elands Bay Cave allows further discussion of the value of John Parkington’s pivotal concept of ‘place’ and of the merits and disadvantages of employing ‘industries’ as building blocks for thinking about the hunter-gatherer past. New fieldwork in Lesotho reinforces this, along with the importance of deepening the relation between theory and the process of archaeological excavation itself.
A richer, better-resolved dataset allows both ‘social’ and ‘ecological’ perspectives to be explored in greater detail than is possible for earlier periods. Themes discussed include regionalisation in material culture, the development of formal burial, shifts in exchange networks, changes in landscape use and subsistence, fluctuations in regional demography, and potential indicators of socio-economic intensification. This last point raises the question of how ‘complex’ southern Africa’s hunter-gatherer societies were and whether social and/or environmental constraints inhibited the emergence of food production using indigenous resources. Recent improvements in dating now offer the possibility of drawing southern Africa’s rich hunter-gatherer rock art into temporally anchored conversations with other components of the archaeological record. The chapter shows that Bushman ethnography strongly supports interpretations of that art in terms of beliefs and practices associated with shamanism, but that new theoretical work (notably studies employing the ‘new animism’) and further work on gender and initiation continue to expand how it can be understood.
This chapter looks at the profound advances made over the past two decades or so in our understanding of modern human origins, of how humans lived in southern Africa during Marine Isotope Stages 6−4, and of their cognitive capacities. While genetics and palaeontology cannot establish a central role for southern Africa in H. sapiens’ emergence, the region provides the most detailed early evidence anywhere for a wide range of complex behaviours that speak to the cognitive abilities of those responsible for them: art, jewellery, bone tools, archery, pigment manufacture, pyrotechnology, snaring and trapping of small game, etc. Much of this material is associated with the Still Bay and Howiesons Poort industries and the significance of this is discussed along with how southern Africa’s record relates to the wider Palaeolithic context in Africa and Eurasia. While underlining the importance of sites like Blombos, Border Cave, Klasies River, Pinnacle Point, and Sibhudu, the chapter emphasises the limitations of (near-)coastal/Fynbos Biome-oriented research and the increasing importance of fieldwork in other regions, such as Namaqualand, the southern Kalahari, and highland Lesotho.
This chapter looks at the establishment of farming communities in the east of southern Africa within the broader context of agropastoralist expansion south of the Equator and the spread of Bantu languages. Much of the literature on this topic depends heavily on analysis of ceramic design and arguments linking variation in this to variation in broad ethnolinguistic affiliations. The cultural-historical framework based on this is discussed, but alternative methods of ceramic classification are also explored, while the antiquity and utility of the Central Cattle Pattern settlement structure and its cognitive associations are critically assessed. In their dependence on a direct historical approach that is projected far back into the past both questions provide an agriculturalist counterpoint to the use of Bushman ethnography for understanding archaeological hunter-gatherer societies. Beyond these more theoretical concerns, Chapter 10 also emphasises the role of metallurgy, the social relations and subsistence base of early farming societies, the start of their engagement with Indian Ocean trade networks, and their interactions with pre-existing forager communities.
Neither southern Africa’s archaeology nor its history or contemporary social and political structure can be understood without reference to its experience of colonialism and conquest or of the resistance to this. This chapter therefore looks at the archaeology of Portuguese exploration and subsequent settlement in Mozambique, as well as at the much more expansive colonisation of southern Africa set in motion by the establishment of a Dutch East India Company (VOC) base at Cape Town in 1652. It traces the spread of European settlement into the region’s interior, the emergence of new creolised populations on and beyond the frontiers of that settlement, the institutionalisation of the social, economic, and political structures that led to apartheid, and – crucially – the resistance of Indigenous societies to this. Chapter 13 also discusses the Mfecane and the emergence of the Zulu, Basotho, Ndebele, and Swazi states, among others, to emphasise their contemporaneity and potential connections with European settler expansion and to encourage comparative study of processes of state formation, migration, and population incorporation common to both.
Just as the archaeology of the Zimbabwe Culture’s later phases (the Torwa and Mutapa states) can be understood as an exercise in historical archaeology structured by dialogue between the evidence of material culture and that of oral and written histories, so too can the recent past of farming communities and their neighbours south of the Limpopo. Here (and extending into modern Botswana), the archaeological record of the past several hundred years is that of the ancestors of today’s Sotho/Tswana, Nguni, Tsonga, and Venda peoples. This chapter therefore looks at the expansion of farming populations on to the temperate grasslands of South Africa’s interior; the multiple interactions between farmers, pastoralists, and hunter-gatherers (something also increasingly informed by genetics); early contacts with European traders on southern Africa’s Indian Ocean coast; the creative potential of cattle, metals, and other indigenous resources to generate power and wealth; the emergence of more complex societies and denser patterns of settlement; and the construction of new built landscapes that are only now beginning to be understood in detail (notably in Mpumalanga and Gauteng).
Returning to some of the themes addressed in Chapter 3, this final chapter considers the wider social responsibilities of archaeologists working in southern Africa in the twenty-first century. Matters discussed include gender and racial equity within the discipline itself (especially with respect to South Africa), how best to relate the work done by archaeologists to the wider public, heritage management and conflicts over this (including the restitution of cultural sites, property, and human remains), the roles of contract archaeology, university teaching departments, and museums, the importance of publication, and the potential for developing post-colonial approaches to the interpretation of archaeological evidence. In highlighting possible future research trends, the chapter concludes by emphasising the need for work that is both intellectually sound and socially engaged and by reiterating the global significance of southern Africa’s immensely long and varied archaeological record.
This chapter sets out some of the key frameworks within which southern African archaeology operates. It first establishes the boundaries of ‘southern Africa’ for the purposes of this book and then examines the region’s physical geography. The climate and topography described frame southern Africa’s present-day ecology, which is discussed using the biome divisions of Mucina and Rutherford (2006). The chapter then considers how environmental change affected southern Africa during the Quaternary (using the well-known Marine Isotope Stage (MIS) system), the data that archaeologists and others use to reconstruct past environments, and the principal climatic mechanisms at work in the region. It concludes by outlining and assessing the major chronometric and other dating methods employed to build the chronological framework of southern Africa’s past.