Professor Simon Underdown
BSc, PCTHE, PhD (Cantab), CSciTeach, FSA, FRSB, FRGS, FRAI, FCPS, SFHEA
Professor of Biological Anthropology
School of Law and Social Sciences
Role
Please visit my website for more information:
Research
Centres and institutes
Groups
Projects
- Human-Disease Co-Evolution in Deep Time
Projects as Principal Investigator, or Lead Academic if project is led by another Institution
- DNA and The Ancient Flora of Oman: A Research and Training Partnership (01/01/2021 - 31/12/2023), funded by: The Anglo-Omani Society, funding amount received by Brookes: £45,000
- sedaDNA, Environmental Changes and Demography In Oman (01/09/2019 - 31/07/2024), funded by: Society of Antiquities of London, funding amount received by Brookes: £14,907
Publications
Journal articles
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Truter, M, Koopman, J, Jordaan, K, Tsamkxao, L, Cowan, D, Underdown, S, Ramond, J,Rifkin, R, 'Documenting the diversity of the Namibian Ju|’hoansi intestinal microbiome'
Cell Reports 43 (2) (2024)
ISSN: 2211-1247 eISSN: 2211-1247AbstractPublished here Open Access on RADARWe investigate the bacterial and fungal composition and functionality of the Ju|’hoansi intestinal microbiome (IM). The Juǀʼhoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|’hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|’hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
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Houldcroft CJ, Underdown SJ, 'Infectious disease in the Pleistocene: Old friends or old foes?'
American Journal of Biological Anthropology [online first] (2023)
ISSN: 2692-7691 eISSN: 2692-7691AbstractPublished here Open Access on RADARThe impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of Van Blerkom (2003), Wolfe et al (2007) and Houldcroft & Underdown (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travellers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Bretzke K, Preusser F, Jasim S, Miller C, Preston G, Raith K, Underdown SJ, Parton A, Parker AG, 'Multiple phases of human occupation in Southeast Arabia between 210,000 and 120,000 years ago'
Scientific Reports 12 (2022)
ISSN: 2045-2322 eISSN: 2045-2322AbstractPublished here Open Access on RADARChanging climatic conditions are thought to be a major control of human presence in Arabia during the Paleolithic. Whilst the Pleistocene archaeological record shows that periods of increased monsoon rainfall attracted human occupation and led to increased population densities, the impact of arid conditions on human populations in Arabia remains largely speculative. Here, we present data from Jebel Faya in Southeast (SE) Arabia, which document four periods of human occupation between c. 210,000 and 120,000 years ago. The Jebel Faya record indicates that human occupation of SE Arabia was more regular and not exclusively linked to major humid periods. Our data show that brief phases of increased rainfall additionally enabled human settlement in the Faya region. These results imply that the mosaic environments in SE Arabia have likely formed a population refugia at the end of the Middle and the beginning of the Late Pleistocene.
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RF Rifkin, S Vikram, J-B Ramond, A Rey-Iglesia, TB Brand, G Porraz, A Val, G Hall, S Woodborne, M Le Bailly, M Potgieter, SJ Underdown, JE Koopman, DA Cowan, Y Van de Peer, E Willerslev, AJ Hansen, 'Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo- faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome'
Microbiome 8 (2020)
ISSN: 2049-2618 eISSN: 2049-2618AbstractPublished here Open Access on RADARBackground
The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.Methods
Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.Results
Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to ‘Western’ diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.Conclusions
Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. -
Houldcroft CJ, Rifkin RF, Underdown SJ, 'Human biology and ancient DNA: exploring disease, domestication and movement'
Annals of Human Biology 46 (2) (2019) pp.95-98
ISSN: 0301-4460 eISSN: 1464-5033Published here Open Access on RADAR -
Ham E, Underdown SJ, Houldcroft CJ, 'The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans'
Annals of Human Biology 46 (2) (2019) pp.99-108
ISSN: 0301-4460 eISSN: 1464-5033AbstractPublished here Open Access on RADARBackground. Simoni et al (2016) reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious but can also help prevent blood loss. We investigated two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Results. Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. National census data indicates a positive correlation between presence of rs3917862 and decreased maternal mortality ratios. When maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion. These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.
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Pimenoff VP, Houldcroft CH, Rifkin RF, Underdown SJ, 'The Role of aDNA in Understanding the Co-Evolutionary Patterns of Human Sexually Transmitted Infections'
Genes 9 (7) (2018)
ISSN: 2073-4425AbstractAnalysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale; and to estimate the diversity, distribution and co-evolutionary host-relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies, and ancient samples, yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide e.g. through shared data.Open Access on RADAR -
Underdown, SJ Kumar, K Houldcroft, CJ, 'Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data'
Virus Evolution 3 (2) (2017)
ISSN: 2057-1577AbstractHerpes simplex virus 2 is a human herpesvirus found worldwide that causes genital lesions and more rarely causes encephalitis. This pathogen is most common in Africa, and particularly in central and east Africa, an area of particular significance for the evolution of modern humans. Unlike HSV1, HSV2 has not simply co-speciated with humans from their last common ancestor with primates. HSV2 jumped the species barrier between 1.4 and 3 MYA, most likely through intermediate but unknown hominin species. In this paper, we use probability-based network analysis to determine the most probable transmission path between intermediate hosts of HSV2, from the ancestors of chimpanzees to the ancestors of modern humans, using paleo-environmental data on the distribution of African tropical rainforest over the last 3 million years and data on the age and distribution of fossil species of hominin present in Africa between 1.4 and 3 MYA. Our model identifies Paranthropus boisei as the most likely intermediate host of HSV2, while Homo habilis may also have played a role in the initial transmission of HSV2 from the ancestors of chimpanzees to P. boisei.Published here Open Access on RADAR -
Veldhuis D, Underdown S, 'Human Biology of Migration'
Annals of Human Biology 44 (5) (2017) pp.393-396
ISSN: 0301-4460 eISSN: 1464-5033Published here Open Access on RADAR -
Houldcroft CJ, Ramond J, Rifkind RF, Underdown SJ, 'Migrating microbes: What pathogens can tell us about population movements and human evolution'
Annals of Human Biology 44 (5) (2017) pp.397-407
ISSN: 0301-4460 eISSN: 1464-5033AbstractThe biology of human migration can be observed from our co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to our bodies, others have the ability to become life-long human passengers. The story of a pathogen’s genetic code may therefore provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases.Published here Open Access on RADAR
Here, we explore which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. We then present three stories of germs on a journey. The first is the story of HIV’s spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2.
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Houldcroft C, Underdown S, 'Neanderthal genomics suggests a Pleistocene time frame for the first epidemiologic transition'
American Journal of Physical Anthropology 160 (3) (2016) pp.379-388
ISSN: 0002-9483 eISSN: 1096-8644AbstractPublished here Open Access on RADARHigh quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases, or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between human populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone.
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Underdown S, Oppenheimer S J, 'Do patterns of covariation between human pelvis shape, stature, and head size alleviate the obstetric dilemma?'
Proceedings of the National Academy of Sciences 113 (3) (2016)
ISSN: 0027-8424 eISSN: 1091-6490Published here Open Access on RADAR -
Underdown S J, 'Fitzroy's fighting Fuegians: comparisons of palaeopathological and ethnographic indications of fighting behaviour in an extinct human population'
International Journal of Osteoarchaeology 22 (3) (2010) pp.373-378
ISSN: 1047-482X eISSN: 1099-1212AbstractThe Selk'nam were an indigenous population of Tierra del Fuego that are now extinct. Contemporary accounts, including those of Robert Fitzroy and Charles Darwin, attest to their prodigious size and strength. These accounts and others record that the Selk'nam were enthusiastic wrestlers and fought till one or other of the opponents could no longer continue. Presented here is a case of traumatic injury to the ulnae and radii of a Selk'nam male that is concomitant with injuries sustained during such activity and as such would provide intriguing evidence of this practice in the skeletal record of an extinct human population.Published here -
Priston N E C, Underdown S J, 'A simple method for calculating the liklihood crop damage by primates: an epidemiological approach'
International Journal of Pest Management 55 (1) (2009) pp.51-56
ISSN: 0967-0874 eISSN: 1366-5863AbstractPublished hereHuman-wildlife conflict, specifically crop raiding by wildlife, is an increasing concern. Primates are a particular problem across much of Africa and Asia, especially for rural, subsistence farmers living and farming at the forest edge. Most methods designed for sampling and extrapolating from primate crop damage in a subsistence farming context require extensive data collection and involve considerable expenditure of time to complete data analysis. Using a standard epidemiological model, we predict the relative risk of primate crop raiding based on crops grown, their availability within individual farms and patterns of primate selectivity. The model produces an index of relative risk of crop raiding by primates within a geographical region. It rapidly ranks farms according to their vulnerability to crop raiding, with limited need for in-depth data collection. It will therefore allow a more effective deployment of protection methods and more pro-active targeting of resources. This method of modelling primate crop damage can be taught to local communities rapidly and easily. Although not designed to replace existing methods, it can run effectively in conjunction with them.
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Underdown S J, 'A potential role for transmissible spongiform encephalopathies in neanderthal extinction '
Medical Hypotheses 71 (1) (2008) pp.4-7
ISSN: 0306-9877AbstractThe Neanderthals were a Eurasian human species of the genus Homo that disappeared approximately 30,000 years ago. The cause or causes of their extinction continues to intrigue specialists and non-specialists alike. Here a contributory role for Transmissible Spongiform Encephalopathies (TSEs) is suggested. TSEs could have infected Neanderthal groups as a result of general cannibalistic activity and brain tissue consumption in particular. Further infection could then have taken place through continued cannibalistic activity or via shared used of infected stone tools. A modern human hunter-gatherer proxy has been developed and applied as a hypothetical model to the Neanderthals. This hypothesis suggests that the impact of TSEs on the Neanderthals could have been dramatic and have played a large part in contributing to the processes of Neanderthal extinction.Published here -
Underdown S, 'A Comparative Approach to Understanding Neanderthal Trauma'
Periodicum Biologorum 108 (2006) pp.485-493
ISSN: 0031-5362
Book chapters
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Parker AG, Underdown SJ, 'Environmental Controls on Human Dispersal and Adaptation' in Pollard AM, Armitage RA, Makarewicz CA, (ed.), Handbook of Archaeological Sciences, Wiley (2023)
AbstractPublished hereHuman dispersals and adaptations are the result of the dynamic relationship between cultural and biological systems. This chapter focuses on the last half a million years with an emphasis on the environmental controls on human dispersal and adaptation, with the perspective of spatiotemporal variations in environments as a key factor. It provides a brief overview of landscapes and their complexity and controls over time and space. Human dispersals and adaptations require an understanding of complex interactions and strong couplings that link human dynamics, biology, biochemistry, geochemistry, geology, hydrology, geomorphology, and atmospheric dynamics, including climate change. The literature is increasingly full of proposals about environmental barriers, glacial/interglacial cycles, sea-crossings, land bridges, and adaptive specializations, but they often lack the means to evaluate their individual and combined impacts on hominid dispersal. The chapter highlights aspects relating to examples of three of these, namely sea level variations, deserts, and mountains.
Conference papers
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Smith S, Underdown S, 'Lifting the Gloomy Curtain of Time Past: Tracing the Identity of the First Cognitively Modern Hominin in Deep History'
(2019)
ISBN: 9781912385034
Reviews
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Davies R, Underdown S, review of The Neanderthals: a Social Synthesis
Cambridge Archaeological Journal 16 (2006) pp.145-164
ISSN: 0959-7743 eISSN: 1474-0540Published here
Other publications
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Underdown S, 'How the Word Hominid Evolved to Include Hominin', (2006)
Published here -
Davies R, Underdown S, 'Some Observations on the Neanderthals - a Social Synthesis (davies and Underdown Cambridge Archaeological Journal 16.2 (june) 2006, 145-64) - Response', (2006)