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aRNA: A Helpful Friend In Palaeopathology?

20 Dec

It is another quick post from me highlighting another researcher’s work but it is one well worth reading!  Over at So Much Science, So Little Time researcher Dr Kristin Harper has highlighted an intriguing possibility on the direction for the future of palaeopathology.

What is aRNA?

Harper’s post highlights the possible value of aRNA ( ancient Ribonucleic acid) in the investigation of viruses (think influenza and coronaviruses such as SARS) in past human populations in her post on the ability of researchers being able to obtain aRNA samples from 700 year old maize samples.  RNA performs a variety of important functions in the coding, decoding, regulation and expression of genes; essentially RNA acts as the messenger which carries instructions from DNA (Deoxyribonucleic Acid) for controlling the synthesis of proteins in living cells.  DNA itself is the molecule that encodes the genetic instructions that are used in the development and functioning of all known living organisms (including many viruses) however, unlike DNA, RNA is composed of shorter single strands of nucleic acids.  This has made it particularly vulnerable to degradation in archaeological contexts.

The best place to search for evidence of aRNA strands in the human skeleton in an archaeological context would be in the dental pulp cavity, specially the molar teeth.  This seems to be the place where diagenesis  has the least effect on the human skeleton due to both the tough enamel coating found in human teeth and the tooth sockets themselves being fairly protected inside the mandible and maxilla, which is where cortical bone is often dense due to the biomechanics of mastication (Larsen 1997).

I should point out here that the area of genetics is not my specialty but it is an area of inherent interest for me, especially in its applications to palaeoanthropology and palaeopathology.

Why Could This Be Important?

The foundations of palaeopathology are built on the observed changes in human skeletal material and palaeopathology itself often specifically focuses on markers of stress or trauma that can be found in the macro or micro skeletal anatomy.  As a consequence of this many diseases (and indeed traumas) are ‘invisible’ in the archaeological record as they leave no marker of note on the skeleton itself.  The diseases and syndromes that do leave a lesion (which can include blastic and/or lytic lesions) are often said to leave pathognomonic lesions that are, at a basic level, an indicator of the disease or infection processes behind the bone change.

So, as you can imagine, quite often in human osteology we have a ‘healthy’ skeleton of an individual that has died at such and such an age but with no obvious cause of death.  In essence we have the osteological paradox, where those who do contract a disease and die shortly afterwards leave no evidence of bone lesions (or trace of the cause of death) in comparison to individuals who do have severe pathological bone changes but have evidently lived long enough for the disease itself to alter the skeletal architecture; it is, in short, the question of discerning the health of a past population (Larsen 1997: 336).  This is a simplified version of the osteological paradox, a discussion outlining the paradox and it’s full implications and discussion points can be found in Woods et al.’s (1992) article (available online here).

This can have serious effects on our estimates of disease prevalence in history and prehistory, especially in the cases of viruses as they can often kill quickly and leave no skeletal marker.  However because they are cells that were once alive they do leave behind evidence of traces of aRNA.  So any new methodology of being able to extrapolate aRNA of past infections from human skeletal material is welcome as this could potentially open up new insights into past populations and population dynamics.

Further Information


Larsen, C. 1997. Bioarchaeology: Interpreting Behaviour From The Human Skeleton. Cambridge: Cambridge University Press.

Woods, J. W., Milner, G. R., Harpending, H, C. & Weiss, K. M. 1992. The Osteological Paradox: Problems of Inferring Prehistoric Health from Skeletal Samples. Current Anthropology. 33 (4): 343-370. (Open Access).

Dental Delights and Disability in Archaeology

26 Mar

I’ve recently had the joy of a dealing with a dental abscess affecting the left hand side of my mandible, and whilst I’m thankful for modern medicine I can only imagine the pain and frustration for pre-modern populations suffering with such an infection, especially those who didn’t have access to antibiotics and strong painkillers.  As such I haven’t posted properly for a while, and it might be a bit longer before I do.  Having had surgery to relieve the effect of the swelling and to drain the infection and remove two pesky teeth (with added complications courtesy of Fibrous Dysplasia), I’m once again learning how to chew (farewell 1st and 3rd left mandibular molars!).  It has also given me the time to think about the role of disability in the archaeological record and how it is approached by modern-day researchers.  What follows below is a very quick and brief overview of the main points of how disability has been approached in the archaeological sector and the changes therein.  Articles of interest are noted in the bibliography.

Dettwyler famously wrote a paper entitled ‘Can paleopathology provide evidence for compassion‘ (1991: 375-384, PDF embedded) that rightly questioned the interpretations of archaeologists and osteologists on the inferred aspects of care and compassion that disabled individuals from the archaeological record may or may not have received during their lifetimes.  The author cautioned that archaeologists and researchers are not ‘justified in drawing conclusions either about quality of life for disabled individuals in the past or attitudes of the rest of the community from skeletal impairment of physical impairment’ (Dettwyler 1991: 375).  This was a much-needed wake up call, and rightly raised questions in the realms of archaeology and palaopathology regarding how we viewed individuals, and how we analysed them.

The majority of disability studies before the Dettwyler (1991) article focused on disabled individuals as case studies, reported in journals and rarely integrated or investigated as part of the society or cemetery population they may belonged to.  Mays (2012) rightly investigated the impact of the relative value of individual case studies compared to quantitative and problem orientated population studies, and found that although the publishing gap had lessened between the two types, singular case studies still predominated.  Mays (2012) main contention is that individual case studies do little to further the advance of palaeopathology, something which Larsen (1997) effectively demonstrates throughout his book and review (2002), in the consideration of how palaeopathology can indicate society or cultural wide rituals, actions or lifestyles.

Since the publication of the Dettwyler paper there has been a slew of articles, journals and books dedicated to researching disability as evidenced from the skeletal and archaeological record, both from a bioarchaeological perspective and from a theory perspective (Battles 2011, Brothwell 2010, Hawkey 1998, Kleinman 1972, Vilos 2011, Wood et al. 1992).  Indeed the study of disability and the implications for affected individuals, their communities and societies, has moved on considerably since the descriptive days of Calvin Wells, especially in the consideration of the theory of ‘compassion’ as an evolutionary force in the primate family (Hublin 2009, Stewart et al. 2012), or as evidenced in other mammals (Fashing & Nyuyen 2011).

This is in accordance with the rise and debate of disability theory and studies in numerous other disciplines.  This has had real life applications in many areas of modern-day life, where multi-agented approaches to understanding,  recognising and implementing programs that are designed to raise awareness or life quality for disabled individuals.  Two prominent examples from the UK are the 2005 Disability Discrimination Act and the 2010 Equality Law where disability itself is given a legal definition, and here we come to a prominent problem in the archaeological and palaeopathological record itself.

Disability, as we would recognise it today, can mean both a physical and/or a mental impairment that can be substantial and lifelong, and it is worth noting some problems inherent in the archaeological record.  Firstly, in the archaeological record, we can only recognise physical disability when it has affected the skeletal remains of individuals, normally at a late and severe stage in the disease progression (Aufderheide & Rodriquez 1998, Waldron 2009, Wood et al. 1992).  As such, a large number of individuals with diseases or traumatic injuries that only affected the flesh will go unknown, and as such are unstudied.  Secondly, there is no universal or standard definition of disability that archaeologists and researchers use, it is solely up to the person/persons to define clearly and openly which definition they are using at the outset of their research (and there are a lot of definitions and models depending on which source you base your definition on).  Thirdly, the usage of terminology itself, such as the very word disability, can have vastly different connotations or implications for different populations and cultures (Battles 2011).

There may have been distinct differences as to who was considered disabled or not in historic and prehistoric cultures, and we should, as researchers, always be aware of observer bias ourselves (Dettwyler 1991).  As such researchers should always be clear who they are addressing, and the possible differences highlighted, where evidence is available, as to how a disabled person was treated within their culture when archaeological or cultural evidence is available.

To complicate the matter further is the ‘osteological paradox‘, as highlighted by Larsen (1997), Woods et al. (1992) and Wright & Yoder (2003) amongst others, which heavily influences the health status of skeletal remains that survive and that are then studied.  Therefore it should always be understood that no skeletal sample is entirely representative of their population, that there are many caveats (Hahn 1995, Roberts 2000).

Battles (2011) highlighted the need to move towards a more holistic approach to disability, to take advantage of different fields (including physical anthropology, sociocultural anthropology, experimental studies and archaeology itself) to understand disability at archaeological sites and affected individuals, to a model that integrates the data and insight of the various fields.  In particular Battles (2011) makes the salient point of noting the individuals  (largely females and sub-adults) that historically have been under-studied in archaeological and population analyses.

An important methodological update has been the advancement of a ‘Bioarchaeology of Care‘, as espoused by Tilley & Oxenham (2011), where a four stage assessment of an individual produces an assessment of the care needed for the disabled individual found in a Neolithic Vietnam community.  The stages are: (1) describing,  diagnosing and documenting the individual and site, (2) identify the clinical/functional impacts of disease or trauma, and determine if care was needed, (3) produce a model of care, and finally (4) interpret the implications for the individual and society, as well as possible indications for the identity and nature of both (Tilly & Oxenham 2011: 36).  It could be argued that other researchers have espoused the same sentiments (Roberts & Manchester 2010, Vilos 2011), but it is the clear initiation of the applying the model to individuals who fit the criteria that will hopefully produce further studies and elicit meaningful result which highlight this recent study as one to watch.  The Tilley & Oxenham (2011) model is particularly useful for prehistoric cases where there are no written or documentary sources.

Hawkey’s (1998) study of musculoskeletal markers (MSM’s) of a disabled individual from a New Mexico Pueblo culture highlighted the worth of applying existing osteological techniques to disabled individuals in order to assess the quality of bodily movement.  The modelling of the movement capable for this individual suggested that bodily manipulation, feeding, and the cleaning of this person was likely carried out by members of his culture (possibly family relatives, although this is conjecture) due to the severity of his disability (Hawkey 1998: 330).  Craig & Craig (2011) make extensive use of modern medical imaging to diagnosis a specific disease (fibrous dysplasia) in the case of a sub-adult from an English Anglo-Saxon site.  The striking bone expansion in the mandible is discussed within the social sphere of the community that the individual belonged.  The implications, via the the inference of position of the body within the grave, grave goods and grave location, and studies into Anglo-Saxon culture and social stratification give rise to the theory that the individual was not treated any differently due to his disability, although it is unknown if the disease led to the early demise of the individual (Craig & Craig 2011: 3).

Craig & Craig’s (2011) case study, and the above studies, highlight the use of modern medical literature and imaging technology in establishing a likely disease diagnosis, yet Brothwell (2010) rightly highlights the dangers of the differential diagnosis of diseases in skeletal remains at a macroscopic level.  Waldron’s (2009) palaeopathology handbook presents an ideal source on how to identify diseases that can lead to disability, but highlights the value of the differential diagnosis when the osteologist cannot be exactly sure of the disease.

The battery of scientific techniques used in archaeological investigations, including aDNA analysis, trace chemical analysis, and isotopic analysis amongst others, have become significantly refined within the past two decades, and are now allowing for a more nuanced understanding of individual and population dynamics (Brown & Brown 2011).  This includes the ability to analysis the movement of a person in a landscape within their lifetime (Marstellar et al. 2011), and to understand the changes in diet and the effects of diet on the body (Larsen 1997, Roberts 2000, Roberts & Manchester 2010). It also includes the ability to indicate the likely exposure of populations to various chemicals and diseases (Barnes et al. 2011), and exploration of how social structure (Bentley et al. 2012), and hence the role of the population or of the individual, changed through time.

Perhaps what the above studies cannot show, especially in prehistoric societies, are the actions of the disabled individuals themselves.  It is most likely that we will never know if they took an active interest in their society, if they took part, or how they felt as disabled individuals, or even if they saw themselves as disabled (Battles 2011, Hahn 1995).  Compassion  itself cannot be excavated (Dettwyler 1991), but with careful examination of the available evidence results can be produced that suggest that severely disabled individuals did survive past natural limitations.

The progress continually being made in the hard sciences and in the humanities continues to advance our knowledge of past populations via their skeletal remains and their cultural context.  The understanding of disability within an archaeological and osteological context provides the opportunity to investigate of how individual’s survived, and whether care was a key component (Hawkey 1998, Kleinman 1978, Tilley & Oxenham 2011).  This is a burgeoning area of bioarchological research, and when combined with a multidisciplinary approach, it opens up a wide range of interesting and diverse approaches and avenues.

Case Studies, Theories and Further Information:

Full articles are linked where possible, although a number hide behind Journal pay walls.

Aufderheide, A. C. & Roderiquez-Martin, C. 1998. The Cambridge Encyclopedia of Human Palaeopathology. Cambridge: Cambridge University Press.

Barnes, I., Duda, A., Pybus, O. G. & Thomas, M. G. 2011. Ancient Urbanization Predicts Genetic Resistance to Tuberculosis. Evolution. 65 (3): 842-848.

Battles, H. 2011. Toward Engagement: Exploring the Prospects for an Integrated Anthropology of Disability. Explorations in Anthropology. 11 (1): 107-124.

Bentley, R. A., Bickle, P., Fibiger, L., Nowell, G. M., Dale C. W., Hedges, R. E. M., Hamiliton,. J., Wahl, J., Francken, M., Grupe, G., Lenneis, E., Teschler-Nicola, M., Arbogast, R-M., Hofmann, D. & Whittle, A. 2012. Community Differentiation and Kinship Among Europe’s First Farmers. Proceedings of the National Academy of Sciences Early Edition. 1-5. (Early View).

Brothwell, D. 2010. On problems of Differential Diagnosis in Palaeopathology, as Illustrated by a Case from Prehistoric Indiana. International Journal of Osteoarchaeology. 20: 621-622.

Brown, T. & Brown, K. 2011. Biomolecular Archaeology: An Introduction. Chichester: Blackwell Publishing.

Churchill, S. E., Franciscus. R. G., McKean-Peraza, H. A., Daniel, J, A. & Warren, B. R. 2009. Shanidar 3 Neandertal Rib Puncture Wound and Palaeolithic Weaponry. Journal of Human Evolution. 57: 163-178.

Craig, E. & Craig, G. 2011. The Diagnosis and Context of a Facial Deformity from an Anglo-Saxon Cemetery at Spofforth, North Yorkshire. International Journal of Osteoarchaeology. (Early View doi: 10.1002/oa.1288).

Dettwyler, K. A. 1991. Can Palaeopathology Provide Evidence for “Compassion”? American Journal of Physical Anthropology. 84: 375-384.

Fashing, P. J. & Nguyen, N. 2011. Behaviour Towards the Dying, Diseased, or Disabled Among Animal and its Relevance to Palaeopathology.  International Journal of Palaeopathology. 1: 128-129. 

Hahn, R. A. 1995. Sickness and Healing: An Anthropological Perspective. New Haven: Yale University.

Hawkey, D. E. 1998. Disability, Compassion and the Skeletal Record: Using Musculoskeletal Stress Markers (MSM) to Construct an Osteobiography from Early New Mexico. International Journal of Osteoarchaeology. 8: 326-340.

Hublin, J. J. 2009. The Prehistory of Compassion. Proceedings of the National Academy of Sciences. 106 (16): 6429-6430.

Kleinman A. 1978. Concepts and a Model for the Compassion of Medical Systems as Cultural Systems. Soc Sci Med. 12: 85-93.

Knusel, C. J. 1999.  Orthopaedic Disability: Some Hard Evidence. Archaeological Review Cambridge. 15: 31-53.

Larsen, C. 1997. Bioarchaeology: Interpreting Behaviour from the Human Skeleton. Cambridge: Cambridge University Press.

Larsen, C. S. 2002. Bioarchaeology: The Lives and Lifestyles of Past Peoples. Journal of Archaeological Research. 10 (2): 119-166.

Marstellar, S. J., Torres-Rouff, C. & Knudson, K. J. 2011. Pre-Columbian Andean Sickness Ideology and the Social Experience of Leishmaniasis: A Contextualised Analysis of Bioarchaeological and Palaeopathological Data from San Pedro de Atacama, Chile. International Journal of Palaeopathology. 1 (1): 23-34.

Mays, S. 2012. The Impact of Case Reports Relative to Other Types of Publication in Palaeopathology. International Journal of Osteoarchaeology. 22: 81-85.

Roberts, C. A. 2000. ‘Did They Take Sugar? The Use of Skeletal Evidence in the Study of Disability in Past Populations’. In Hubert, J. (ed) Madness, Disability and Social Exclusion: The Archaeology and Anthropology of Difference. London: Routledge. 46-59.

Roberts, C. & Manchester, K. 2010. The Archaeology of Disease. Stroud: The History Press.

Stewart, F.A., Piel, A.K., O’Malley, R.C., 2012. Responses of Chimpanzees to a Recently Dead Community Member at Gombe National Park, Tanzania. American Journal of Primatology. 74: 1–7.

Tilley, L. & Oxenham, M. F. 2011. Survival Against the Odds: Modelling the Social Implications of Care Provision to the Seriously Disabled. International Journal of Palaeopathology. 1 (1): 35-42.

Vilos, J. D. 2011.  Bioarchaeology of Compassion: Exploring Extreme Cases of Pathology in a Bronze Age Skeletal Population from Tell Abraq, U. A. E. Master’s Dissertation. Las Vegas: University of Nevada.

Waldron, T. 2009. Palaeopathology. Cambridge: Cambridge University Press.

Wood, J. W., Milner, G.R., Harpending H. C., & Weiss, K. M. 1992.  The Osteological Paradox: Problems of Inferring Prehistoric Health from Skeletal SamplesCurrent Anthropology 33:  343-370.

Wright, L. E. & Yoder, C. J. 2003.  Recent Progress in Bioarchaeology: Approaches to the Osteological ParadoxJournal of Archaeological Research 11 (1): 43-70. (**An extensive bibliography of articles can be found in the bibliography of this article**).

Infectious Disease Part 2: Malaria and Associated Anaemic Conditions

5 Oct

This second post, and the first part, deal with biomolecular approaches and research studies in detecting  the presence of infectious diseases in human bone from archaeological material.  The recent coming of age of biomolecular techniques, as applied to archaeological material, has provided a rich and complex source of information in helping to uncover how infectious diseases spread in the historic and prehistoric past.  The second post, here, describes recent research focused on Malaria and associated anaemic conditions, including Sickle Cell Anaemia and Thalassaemia.  The first post can be found here.


It has long been realised that malaria can only be recognised in skeletal remains via indirect evidence of presentation of the following pathological lesions- porotic hyperostosis, cribra orbitalia and marrow hypertrophy- which are taken as evidence of the presence of anaemia, the main contributor of mortality in malarial victims (Roberts & Manchester 2010).  However there is no pathognomonic bone lesion for either Plasmodium vivax or P. falciparum, the main human species of malaria causing Plasmodium genus  (Gowland & Western 2012: 303, Roberts & Manchester 2010: 233), and the above skeletal lesions have varying aetiologies including anaemia, osteitis, parasitic infection, and other interrelated deficiency diseases which are still not clearly understood (Gowland & Western 2012: 302).  To securely diagnose malaria in skeletal material, DNA identification of the Plasmodium genus must take place, and even then current Polymerase Chain Reaction (PRC) tests ‘do not appear to be able to amplify routinely the DNA of malaria pathogens from ancient bones’ (Gowland & Western 2012: 302).

Recent immunological techniques to identify antigens have also been used to isolate and identify P. falciparum, although false positives can occur as a result of contamination or diagenetic factors(Gowland & Western 2012: 302).  Gowland & Western (2012) have recently proposed a spatial epidemiological model for malarial spread in Anglo-Saxon England, which highlights the re-surging interest in malaria in the modern context as well as one affecting a past population.  This holistic approach used GIS data with diagnosed porotic hyperostosis in skeletal remains, mosquito (Anopheles atroparvus) habitat information and historical data in presenting a locality data set for malaria infected individuals (Gowland & Western 2010: 304-305).  The modelling of palaeopathological, climatic, and historical data, provides new information on disease range, mechanism of transmission, and infection localities.  However, there are also complicating factors in assessing and diagnosing malaria from other diseases, as noted below (Roberts & Manchester 2010: 234).

Particularly important are two inherited haemolytic anaemia’s, thalassaemia and sickle-cell anaemia, who are characterised by abnormal haemoglobin and increased destruction of red blood cells (Jurmain et al. 2011: 312, Roberts & Manchester 2010: 232).  Thalassaemia is a genetically determined disorder which is caused by a ‘problem of haemoglobin synthesis’ (Roberts & Manchester 2010: 233).  This results in failure or depression of synthesis of the chain, this leads to pale cells with low hemoglobin content which are then rapidly destroyed once formed.  There are three grades of the disease, minor, intermediate and major, the last of which includes severe anemia and possible bone changes; the range of the disease is typically centered in the Mediterranean, Middle East and Far East (Roberts & Manchester 2010: 233).  The importance is that it is seen as an adaptive response to malaria infection through the development of this heritable disease; that the high red blood cell turnover stalls and negates any effect of malarial infection.  Archaeological evidences comes from Greek, Turkish and Cypriot populations deriving from marshy contexts, which are ideal breeding grounds for mosquitoes, the prime vector for malaria (Roberts & Manchester 2010: 233).

Sickle-cell anaemia occurs as a result of the deformation and destruction of red blood cells which leads to over enlargement of bony centres (centered on the skull, pelvis, vertebrae) and over-activity of marrow production as the body produces more red blood cells (Waldron 2009).  This inheritable disease range is mainly located in Central and Eastern African populations who have high rates of the disease, but also affects Indian, Middle Eastern, and Southern European populations (Roberts & Manchester 2010: 234).  Jurmain et al. (2011: 312) remark that the sickle-cell allele hasn’t always been effective in malarial negation in human populations, and primarily came to prominence during the advent of agriculture, and in particular during the last 2000 years in Africa.  The origin of the mutation of the allele responsible, HB5 in haemoglobin, has been dated to 2100 to 1250 years ago in African populations (Jurmain et al. 2011: 312).  Although malaria infection has only relatively recently affected human populations, it has become a powerful selective force that still affects large portions of the world’s population today.

In conclusion, biomolecular approaches to archaeological and osteological remains are vital in unraveling past populations and the natural world (Jurmain et al. 2011).  The interactions between wild and domesticated animals, humans, insects and the environment are a prerequisite for understanding the mode of transmission and virulence of infectious diseases (Barnes et al. 2011, Gowland & Western 2012, Jurmain et. al 2011).  Yet, we must take into consideration the difficulties in understanding infectious disease; examples of the osteological paradox are ever present, understanding the aetiology of bone changes, and the context of genetic differences between populations must be noted whilst PCR amplification, aDNA detection and genome explorations methods must be continually improved for clearer results (Li et al. 2011, Schurch et al. 2011, Spigelman et al. 2012, Tran et al. 2011); this approach must be multidisciplinary in understanding past and present populations (Jurmain et al. 2011, Roberts & Manchester 2010, Waldron 2009).

The modern world has changed, and the boundaries that once protected various human populations has changed dramatically with cheap air travel and vast population movement; this is unprecedented in both history and prehistory, and in population density and scale, but also at the genetic level in human genetic variation (Hawks et al. 2007, Jurmain et al. 2011: 311).  The eradication of smallpox, the Bill and Melinda Gates foundation in fighting malaria, and the ongoing WHO (World Health Organisation) case against polio (Branswell 2012: 50) are strong examples of what can be achieved worldwide.  By building a past population profile of the effects of infectious disease, we are better prepared for the fight tomorrow.


Barnes, I., Duda, A., Pybus, O. G. & Thomas, M. G. 2011. Ancient Urbanization Predicts Genetic Resistance to Tuberculosis. Evolution. 65 (3): 842-848.

Branswell, H. 2012. Polio’s Last Act. Scientific American. 306 (4): 50-55.

Gowland, R. L., & Western, A. G. 2012. Morbidity in the Marshes: Using Spatial Epidemiology to Investigate Skeletal Evidence for Malaria in Anglo-Saxon England (AD 410- 1050). American Journal of Physical Anthropology. 147: 301-311.

Hawks, J., Wang, E. T., Cochran, G. M., Harpending, H. C. & Moyzis, R. K. 2007. Recent Acceleration of Human Adaptive Evolution. Proceedings of the National Academy of Sciences. 104 (52): 20753-20758.

Jurmain, R., Kilgore, L. & Trevathan, W. 2011. The Essentials of Physical Anthropology, International Edition. Belmont: Wadsworth.

Li, Y., Carroll, D. S., Gardner, S. N., Walsh, M. C., Vitalis, E. A. & Damon, I. K. 2007. On the Origin of Smallpox: Correlating Variola Phylogenics with Historical Smallpox Record. Proceedings of the National Academy of Science. 104 (40): 15787-15792.

Roberts, C. & Manchester, K. 2010. The Archaeology of Disease. Stroud: The History Press.

Schurch, A. C., Kremer, K., Kiers, A., Daviena, O., Boeree, M. J., Siezen, R. J., Smith, N. H., & Soolingen, D. V. 2010. The Tempo and Mode of Molecular Evolution of Mycobacterium Tuberculosis at Patient-to-Patient Scale. Infection, Genetics and Evolution. 10 (1): 108-114.

Spigelman, M., Shin, D. H., & Gal, G. K. B. 2012. The Promise, the Problems and the Future of DNA Analysis in Palaeopathology Studies. In Grauer, A. L. (ed). A Companion to Palaeopathology. Chichester: Blackwell Publishing Ltd.  pp.133-151.

Tran, T., Aboudharam, G., Raoult, D., & Drancourt, M. 2011. Beyond Ancient Microbial DNA: Nonnucleotidic Biomolecules for Palaeomicrobiology. BioTechniques. 50: 370-380.

Waldron, T. 2009. Palaeopathology. Cambridge: Cambridge University Press.

Infectious Disease Part 1: Treponemal Disease & Smallpox

5 Oct

The following two posts deal with biomolecular approaches and research studies in detecting the presence of infectious diseases in human bone from archaeological material.  The recent coming of age of biomolecular techniques, as applied to archaeological material, has provided a rich and complex source of information in helping to uncover how infectious diseases spread in the historic and prehistoric past.  Whilst it has help clear some mysteries up, it has unleashed others.  The first post, here, describes recent research focused on Treponemal diseases (including Yaws, Syphilis and Pinta) and Smallpox.  The second post can be found here.


Treponemal Diseases

Roberts & Manchester (2010: 216) note that infectious diseases are ‘not solely microbiological entities but are a composite reflection of individual immunity, social, environmental, and biological interaction’.  The study of treponemal disease, in particular, is fraught with controversy and stigma, both in the modern and historical contexts (Lucas de Melo et al. 2010: 1, Roberts 2000), and in the nature of its spread and transmission.  However the combination of molecular pathology, phylogenetics, and palaeopathological studies, are helping to produce a clearer genetic origin of the disease and the impacts that this disease had, and continues to have, on the world at large (Hunnius et al. 2007: 2092).  Typically the bacterial diseases of the genus Treponema are split into different forms; pinta (T. carateum), yaws (T. pallidum subspecies pertenue), endemic syphilis (T. pallidum subspecies edemicum) and venereal/congenital syphilis (T. pallidum subspecies pallidum) (Table 1; Lucas de Melo et al. 2010: 2).  The four forms were, until recently, indistinguishable in physical and laboratory characteristics (Roberts & Manchester 2010: 207), whilst the pinta strand does not affect bone (Waldron 2009: 103).  DNA analysis of the bacteria of venereal syphilis has shown a difference between it and the non-venereal types; although it is noted that there is no change in the clinical presentation of the disease (Roberts & Manchester 2010: 207).

Table 1. Geographic location, transmission and whether bone is affected for treponemal disease (after Waldron 2009: 103).

Yaws was likely the first disease to emerge, probably from an ape relative in Central Africa, whilst the endemic form of syphilis derived from an ancestral form in the Middle East and the Balkans at a later date, whilst T. pallidum was the last to emerge, probably from a New World progenitor, although the issue is still highly contentious (Roberts & Manchester 2010: 212, Waldron 2009: 105).  Gaining virulence at a dramatic rate in the 15th and 16th centuries AD in Europe, venereal syphilis affected a large section of the population due to its mode of transmission.  It should be noted, however, that bone changes in syphilis are rare in the early stages but common in the tertiary stage of the disease (Roberts & Manchester 2010).  It has also been noted that there could be a back and forth transmission, from one treponemal disease to another, within intra-population groups changing from one environment to another; that ultimately it’s possible that each social group, or population, has its own treponemal disease suited to its ‘geographic and climatic home and its stage of cultural development’ (Roberts & Manchester 2010: 213).

However, this infectious disease, in its venereal form, is particularly hard to locate and identify in archaeological populations; the limitations of biomolecular palaeopathology have become clear (Bouwman & Brown 2005: 711, Hunnius et al. 2007, Lucas de Melo et al. 2010: 10).  Bouwman & Brown’s (2005) experiment, and Hunnius et al. (2007) subsequent paper, have highlighted the difficulties in amplifying T. pallidum subspecies T. pallidum, even in highly suspected bone samples.  Bouwman & Brown (2005: 711) tested 9 treponemal samples using the Polymerase Chain Reaction (PCR) tests, optimized to highlight ancient treponemal DNA.  This resulted in poor amplification of  treponemal ancient DNA (aDNA) from human bone, even with bone of varying origins (geographic, social and climatic samples).  3 outcomes where postulated; the bones were either not suitable for aDNA retrieval, treponemal aDNA was present but the PCR was not sensitive enough to be pick it up, or there was no treponemal DNA in the bones (Bouwman & Brown 2005: 711-712).  Subsequent investigations and phylogenetic approaches have highlighted that the disease invades different parts of the body at impressive rates, but in the later stages of the disease, the organism’s DNA is not present in the actual bone itself, just at the stage when an osteologist can identify it macroscopically (Hunnius et al 2007: 2098).  Phylogenetic evidence supports evidence of variations in the virulence of syphilis, and the support of a more distant origin, possibly around 16,500 to 5000 years ago, but where exactly remains unsolved (Lucas de Melo et al. 2010: 2).  Interestingly, in the early 20th century P. Vivax (the main causer of malaria) was used as a treatment for patients with neurosyphilis in a procedure by the physician Julius Wagner-Jauregg; it was injected as a form of pyrotherapy to introduce high fevers to combat the late stage syphilitic disease by killing the causative bacteria (Wagner-Jauregg 1931).


The Smallpox virus is particularly devastating and disfiguring disease, but thankfully no longer an active infection in the modern world (Manchester & Roberts 2010: 180).  Although kept only in laboratory samples now, there is an ongoing concern regarding whether it could be a danger to modern archaeologists dealing with infected material (Waldron 2009: 110).  The disease, once contracted, either leads to recovery with lifelong immunity or death.  The severe form is called variola major and is documented in the Old World with a 30% death rate once contracted, whilst its less virulent form, named variola or alastrim minor, is found in Central America and has a mortality rate of 1% (Hogan & Harchelroad 2005, Li et al. 2007: 15788).  Smallpox, the strictly human variola virus pathogen, is found in literature and documentary records during the last 2000 years (Larsen 1997), yet an osteological signature is not present or identifiable in infected individuals (Waldron 2009: 110).  Therefore to find out the origins of the disease, Li et al. (2007) used correlated variola phylogenetics with historical smallpox records to map the evolution, origin and transportation of smallpox between human populations.

Li et al. (2007: 15787) state that no credible descriptions of the variola virus have been found on the American continent or sub-Saharan Africa before the advent of westward European exploration in the 15th century AD; suggesting that with European exploration and expansion came the virulent waves of smallpox that helped to decimate the existing Native American populations, who previously had no contact or natural immunization with such a highly virulent disease.  It is worth noting here the disease has been used in warfare as a chemical weapon surprisingly early.  During the 18th century American colonial wars between the French, British and the Native Americans, the British forces stationed in America actively infected items of clothing that were given to the Native population to help aid the spread of the disease among the Native Americans , who at that time were largely allied to the French.  This weakened the Native American population dramatically during the various colonial wars and subsequent colonial expansion westward; it’s estimated nearly half of the American Native population died from smallpox alone and its naturally rapid commutable spread of smallpox through human populations (Hogan & Harchelroad 2005).

Li et al. (2007: 15787) note that there are ambiguous gaps in the evolution of smallpox disease itself however.  Li et al. (2007) initiated a systematic analysis of the concatenated Single Nucleotide Polymorphisms (SNP’s) from the genome sequences of 47 variola major isolates from a broad geographic distribution to investigate its origins.  Variola major has a slowly evolving DNA genome, which means a robust phylogeny of the disease is possible (Hogan & Harchelroad 2005).

Firstly, the results showed that the origin of variola was likely to have diverged from an ancestral African rodent–borne variola like virus, either around 16,000 or 68,000 thousand years ago dependent on which historical records are used to calibrate the molecular clock (East Asian or African) (Li et al. 2007: 15791).  Taterapox virus is associated with terrestrial rodents in West Africa, and provides a close relationship with the variola virus.  It is entirely possible that variola derived from an enzootic pathogen of African rodents, and subsequently spread from Africa outwards (Li et al. 2007: 15792).  Secondly, evidence points towards two primary clades of the variola virus, both from the same source as above, but each represent a different severity and virulence of the variola virus.

The first primary clade is represented by the Asian variola major strains, which are the more clinically severe form of smallpox;  the molecular study of its natural ‘clock’ suggests it spread from Asia either 400 or 1600 years ago (Li et al. 2007: 15788).  Included in this first primary clade is the subclade of the African minor variation of the main Asian variola major disease.  The second primary clade compromises two subclades, of which are the South American alastrim minor and the West African isolates (Li et al. 2007: 15788).  This clade had a remarkably lower fatality rate in comparison to the above clade.  The importance of phylogeny analysis is that it highlights areas of disease prevalence and virulence that can be missed, or indeed entirely absent, from the osteological and archaeological record (Brown & Brown 2011).


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Brown, T. & Brown, K. 2011. Biomolecular Archaeology: An Introduction. Chichester: Blackwell Publishing.

Hogan, C. J. & Harchelroad, F. 2005. Smallpox. Emedicinehealth. Accessed at on the 29th of April 2012.

Hunnius, T. E., Yang, D., Eng, B., Waye, J. S. & Saunders, S. R. 2007. Digging Deeper into the Limits of Ancient DNA Research on Syphilis. Journal of Archaeological Science 34: 2091-2100.

Larsen, C. S. 1997. Bioarchaeology: Interpreting Behaviour from the Human Skeleton. Cambridge: CambridgeUniversity Press.

Li, Y., Carroll, D. S., Gardner, S. N., Walsh, M. C., Vitalis, E. A. & Damon, I. K. 2007. On the Origin of Smallpox: Correlating Variola Phylogenics with Historical Smallpox Record. Proceedings of the National Academy of Science. 104 (40): 15787-15792.

Lucas de Melo, F., Moreira de Mello, J. C., Fraga, A. M., Nunes, K. & Eggers, S. 2010 Syphilis at the Crossroad of Phylogenetics and Palaeopathology. PLoS Neglected Tropical Diseases.4 (1): 1-11.

Mitchell, P. 2003. The Archaeological Study of Epidemic and Infectious Disease. World Archaeology. 35 (2): 171-179.

Roberts, C. & Manchester, K. 2010. The Archaeology of Disease. Stroud: The History Press.

Wagner-Jouregg, J. 1931. Verhutung und Behandlung der Progressiven Paralyse durch Impfmalaria.  Handbuch der Experimentellen Therapie, Erganzungsband Munchen.

Waldron, T. 2009. Palaeopathology. Cambridge: Cambridge University Press.