Sunday, October 26, 2014

Archaeogenetics: future potential and challenges

I am delighted to introduce the first entrant to the The 2014 Bob Chapple Archaeological Essay Prize in association with Wordwell Books. Stephen Domican's paper Archaeogenetics: future potential and challenges describes his current research and will shortly be appearing in Trowel magazine (Domican, S. (2014) 'Archaeogenetics: future potential and challenges', Trowel, 15, pp. TBC.). If you would like to enter, please check out the criteria at the end of the post: here.


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Archaeogenetics: future potential and challenges

Stephen Domican

Recent developments in the field of genetics, especially next generation sequencing technologies, has set the stage for archaeogenetic research - that is the study of the ancient past using genetic data (Renfrew, 2001) - to become as revolutionary a methodology in archaeological research as the development of radiocarbon dating was in the 1950’s (Taylor, 1995). In 2003, the human genome project successfully completed its 13 year project to completely sequence the human genome, at a cost of nearly $3 billion dollars (Lunshof et al., 2010). The  development of next generation sequencing in 2005 (Knapp and Hofreiter, 2010; Schuster, 2007) brought rapid price decreases, and now the recent release of Illumina's HiSeq X Ten platform claims to allow researchers to sequence the human genome in just three days, at a cost of around $1000 (Sheridan, 2014). With the cost of sequencing an entire genome further predicted to drop down to the $100 mark in the near future (Stein, 2013), archaeological research is set to be radically impacted in the coming decades by the amazing potential of archaeogenetics. In this paper some of the history and potential applications of genetic research in archaeology, along with some of the challenges of effectively interpreting genetic data, will be examined to show how this emergent technology is poised to become a mainstream tool for archaeological research in the not too distant future.


If the 20th century can be seen as the age of the computer, then the 21st is setting itself up as the age of the biologist (Losos et al., 2013). For the past decade a stirring revolution in genetics has seen the constant strive for faster, more efficient and cheaper technology, that is predicted to make genetic technology as important and mainstream a technology as computers have now become (Losos et al., 2013). For years ancient genetic research has been hampered by issues, both technical and cost related, limiting its scope to the select analysis of small sections of the genetic code of samples, such as the mitochondrial DNA (Gilbert et al., 2005; Knapp and Hofreiter, 2010). Now, a series of new genetic sequencing methods collectively known as “next generation sequencing” technologies (Knapp and Hofreiter, 2010; Mardis, 2008; Metzker, 2009), along with new techniques developed to identify ancient DNA from modern DNA contamination (Ginolhac et al., 2011; Skoglund et al., 2014) has ushered in the beginning of a new age of archaeogenetic research: one where highly accurate genetic data can be obtained at a fraction of the cost, and at a scale that was unthinkable only a few years ago (see figure 1). This paper aims to show the importance of ancient DNA research as an archaeological subfield, and will discuss some of the different ways archaeogenetic research can be used by archaeologists to learn about the past. This paper will also discuss some of the challenges that come with interpreting this data, along with touching upon some of the history of ancient DNA research, both how it got to the stage it is currently at, as well as discussing some of the exciting ways new lower cost genetic technology could be applied to archaeological research in the coming years.


Figure 1: Cost per raw megabase of DNA over time compared
with Moore’s law – used with permission from (Jobling and Hurles, 2012)


History
The field of genetic research has seen drastic changes since James Watson and Francis Crick first discovered the double helix structure of DNA in 1953 (Watson and Crick, 1953). Thirty years after their pioneering breakthrough, the field of ancient DNA was born in the mid 1980’s, with the extraction and sequencing of DNA from the quagga, an extinct South African equid, along with the extraction of DNA from an Egyptian mummy sample (Pääbo, 1985; Higuchi et al., 1984). Earlier attempts at DNA extraction were unfortunately often foiled by the lack of appropriate technology to allow scientists to distinguish between endogenous ancient DNA (known as aDNA) and outside sources of DNA contamination (Skoglund et al., 2014).


One of the key developments in genetic studies, the development of PCR (polymerase chain reaction) technology, has allowed geneticists to amplify genetic material for analysis (Jobling and Hurles, 2012, p.95-129). While revolutionary for the field of genetics, PCR did have serious problems for the study of ancient DNA, replicating not only the surviving ancient DNA, but also any contaminating DNA from other exogenous sources present in the sample (Ginolhac et al., 2011). For this reason, many earlier reports of DNA extraction from ancient specimens, and all reports from specimens over a million years old – including all reports of dinosaur DNA (Pääbo et al., 2004) – have been widely dismissed as being the amplified DNA of modern contaminants (Rizzi et al., 2012). The issue of contamination has remained a major issue, with Cooper and Poinar (2000), in their now seminal paper: “Ancient DNA: Do it right or not at all”, openly criticising the lack of contamination control from many practitioners in the field. Simultaneously they suggested a list of standards to be followed, such as having an isolated work area and an outside lab replicate results, which have laid much of the groundwork for modern aDNA standards (Gilbert et al., 2005). These aforementioned contamination issues, as well as high costs, both financial and the time associated with performing the sequencing, have been a limiting factor in the wide-spread application of genetic research to the field of archaeology until now.

Potential applications of genetic research to the field of archaeology
Genetic research is a powerful tool for the archaeologist, and it can be used to look at large, macro-scale questions asked of the past, such as how populations have migrated and reproduced over time (Knapp et al., 2012; Pinhasi et al., 2012; Ralph and Coop, 2013; Veeramah and Hammer, 2014). This is important not only for the information it can potentially tell us about past population movements, but also because it allows us to answer questions relating to the long standing debate of cultural vs demic diffusion (Pinhasi et al., 2012), and whether specific technological and cultural changes primarily occurred due to contact with external cultural groups (cultural diffusion), or if the spread of ideas is down to the migration of people into a new area (demic diffusion).

Genetic research can also be used to analyse archaeological remains at the level of the individual. Past research has shown how the analyses of a wide variety of attributes such as kinship (Deguilloux et al., 2014), diet (Bon et al., 2012; Hofreiter et al., 2001, p.358), individual ethnic descent (Martiniano et al., 2014), health (Leonardi et al., 2012), and even personal information such as hair and eye colour (Lalueza-Fox et al., 2007; Olalde et al., 2014) are now within our technological capability. Of great potential is how genetic research now allows us to look at one of the most essential social units of all: that of kinship. By observing changes in inheritable DNA such as mitochondrial (mtDNA) and Y DNA (non-recombining portion of the Y chromosome: NRY) - passed down from mother and father respectively (Jobling and Hurles, 2012) - as well as by observing changes to other components of the genetic code that are passed from generation to generation (Jobling and Hurles, 2012), archaeologists are now able to research familial relations in a whole new way, through the observation of kinship patterns in the archaeological record.

Population genetics
Both modern and ancient DNA can be used to analyse past population descent and migration. By observing the aforementioned changes in the genetic code, that are inherited, researchers have been able to analyse large scale population migrations, and develop theories as to how migrants interbred with local populations. Most notably this was used to investigate the “out of Africa” theory of how anatomically modern humans originated and migrated from Africa (Veeramah and Hammer, 2014). This model was later expanded upon, with additional analyses suggesting a level of genetic breeding between non-African humans and other species of hominin such as Neanderthals and Denisovans (Huerta-Sánchez et al., 2014; Sankararaman et al., 2014).

Much research in the past decades has focused on the origins and migration of prehistoric populations (Brandt et al., 2013; Pinhasi et al., 2012; Raghavan et al., 2013; Ralph and Coop, 2013; Skoglund et al., 2012), and a particular “hot topic” of examination has been whether the spread of agricultural and other technologies associated with the Neolithic – the so called “Neolithic package” – better fits into the aforementioned cultural or demic model of diffusion. Related work has focused on both analysing the genetic spread of ancient human populations (Pickrell and Reich, 2014) and the genetic signature of the domesticated animals that accompanied them (Cai et al., 2014; Larson et al., 2007), in order to test and develop new migration theories. Indeed, as genetic sequencing costs decrease, large scale population studies will become an increasingly lucrative area of research and it will be exciting to see what future results will uncover.

Researching trade and exchange networks using genetic sampling
Genetic research also allows archaeologists to examine ancient trade and exchange networks, and to deconstruct how organic materials were exchanged. Publication of genetic data obtained from swabs sampled from ancient Greek amphorae, recovered from 5th-3rd century BCE shipwrecks (Foley et al., 2012), serves as a prime example of how previously inaccessible data can be obtained from organic remains hidden within artefacts. This study was able to identify not only the contents of most of the amphorae, which were found to contain a mixture of herbs and olive oil, but was also able to challenge long held assumptions that amphorae were primarily used in the transportation of wine (Foley et al., 2012). The genetic research from this paper was also able to identify new data as to what ancient diet was like, opening up the exciting potential of research into how ancient dietary tastes have co-evolved with trading activity over time.

Indeed, another paper highlighting the use of archaeogentic research in the analyses of ancient trade, published by Arndt et al (2003), looked into ancient smoked catfish (clarias) remains from the Roman/Early Byzantine town of Sagalassos, in Turkey. Using analysis of variations in the mitochondrial DNA, which is inherited only from the female parent (Jobling and Hurles, 2012), the authors were able to identify not only the species of catfish exchanged, but also provenance a probable upper Nile river source for these remains. Although both studies were limited by their use of older – that is, non “next-generation” – sequencing technologies, these publications highlight how archaeogenetic research can be effectively used to research ancient trade of organic materials. Due to the networked nature of exchange, this type of research becomes exponentially more useful once larger data sets are obtained from multiple geographic locations, something which has been previously limited due to prior mentioned cost and technology issues. With increasing attempts to extract ancient DNA from a  wide variety of organic and non-organic materials and remains (King et al., 2009), and the aforementioned trend of decreasing costs and improved technologies suggesting that in the near-future we are likely to see this barrier become less of an obstacle for provenance studies in archaeological research.

Analysis of organic and inorganic ancient material
There is also much potential for genetic research to be applied to the identification of organic remains in archaeological artefacts, both through the identification of previously unknown organic material within artefacts, and through identifying minute genetic information in environmental samples. A number of recent studies have successfully managed to extract ancient DNA from organic materials, such as manuscripts (Poulakakis et al., 2007) and cereal grains (Fernández et al., 2013), in an attempt to identify the species and possible origin. Of particular note is the recovery of ancient DNA from organic material contained within non-organic material such as flint tools (Shanks et al., 2005; Shanks, Kornfeld and Ream, 2004) and ceramics (Foley et al., 2012).

Due to the poor preservation of organic material over time, archaeologists are often faced with an incomplete picture as to how exactly ancient humans interacted with the organic material that comprised a large part of the world around them. By detecting even minute organic remains in artifacts and environmental samples, the field of archaeogenetics is increasingly allowing for more informed research to take place on this interaction between both human and material-culture and human and non-human species.

Challenges in using archaeogenetic research
Although genetic research has seen vast advances over time, there are still many challenges researchers face in order to correctly use this source of data (Gilbert et al., 2005). The challenge is no longer so much in how you extract the data, but in how such large amounts of biological data is computationally handled (Flicek and Birney, 2009; Li and Homer, 2010; Treangen and Salzberg, 2011), along with how researchers interpret this data, that is key to its effective application to archaeological questions. However, issues of contamination are still – and likely will always remain - a concern, and proper protocol to avoid contamination, both at the excavation and later DNA sequencing phase, is a key step to the production of reliable data. This includes provision of the provenance of the sample (Gilbert et al., 2005), the avoidance of excess handling of any archaeological artifacts or organic remains, and the wearing of sterile gloves during handling (Roberts and Ingham, 2008). Proper provenance of an archaeological specimen is particularly important, as older contamination from artifacts and remains excavated decades or centuries prior to examination may exhibit similar DNA damage patterns as endogenous ancient DNA. This older contamination can inhibit aDNA screening techniques that rely on analysing particular damage patterns in ancient DNA in order to correctly differentiate between endogenous ancient DNA and modern contamination (Jobling and Hurles, 2012). Appropriate ethical considerations also need to be taken when working with samples from living human beings, used in the research of past population migrations; prior controversy and legal action has occurred from improper usage of genetic data in research for which the donors did not give prior consent (Reardon and TallBear, 2012).

Indeed, there is now a need for archaeologists to familiarise themselves with genetic research, in order to be able to critically assess which research is up to standard, so that archaeologists can make the decision as to when the destruction of irrecoverable archaeological material consumed in the DNA extraction process is validated. Of concern is the fact that serious criticism has been levelled at much prior ancient DNA research (Gilbert et al., 2005). For example, Roberts and Inham (2008) noted significant issues in the quality of paleopathology papers, studying ancient diseases, observing that out of 65 ancient DNA papers published between 1993 and 2006 that attempted to detect ancient pathogens, 45% of them failed to refer to whether an isolated ancient DNA laboratory had been used in the research, 90% did not discuss excavation procedures of samples, and only 12% of papers reported independent replication of their results as suggested by Cooper and Poinar (2000). Of note is the fact that not on reported paper managed to adhere completely to all listed contamination criteria.

It is also important that archaeologists familiarise themselves with which material is viable for genetic extraction. Genetic degradation is a complex process, occurring due to a number of environmental factors such as temperature and humidity (Smith et al., 2003), and DNA is also believed to survive better in certain bones and remains than in others (Campos et al., 2012). Although samples sizes required for testing are often small, DNA extraction still involves costs, both in terms of the physical damage done to archaeological remains and the financial costs involved in sample extraction. For this reason, much research is currently being undertaken to develop heuristics for which samples should be used in DNA extraction. For example, by calculating the environmental conditions or “thermal age” (Smith et al., 2003) of a sample, researchers are now able to identify the samples which are still likely to contain genetic material, in order to avoid unnecessary waste.

Informed archaeologists, aware of the uses and challenges of genetic research are needed now more than ever, both in order to make the correct decisions as to which samples, if any, are viable for DNA extraction, and that these samples are then used to answer specific archaeological research questions. In order to be able to properly utilise genetic research, archaeologists must develop a critical eye to the validity of any publications involving genetic research in an archaeological context (Gilbert et al., 2005), and whether they have sufficiently designed their research experiment to properly control for outside contamination hazards.

Conclusion
In conclusion, further predictions of increasing technological capacity at a lower cost, along with better sampling methodologies, and novel new applications for archaeogenetic research in analysing non-organic material, is likely to soon make genetic research an increasingly integral component of archaeological research. We are entering an exciting age for archaeological research, as the full potential of genetic technology and large scale, low cost genetic sequencing is still to be fully uncovered.

Acknowledgments
This paper is dedicated to the memory of my recently passed grandfather Séan Bradley, to whom I credit my love of the ancient past, and who encouraged me to write my first publication for the 2013 edition of this journal last year.

I would also like to thank Dr Dan Bradley, and the researchers at the Molecular Population Genetics lab, Trinity College, Dublin, for inviting him to take part in a 5 week internship with them, which served as the inspiration for the article topic. 

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About the author:

Stephen Domican is a final year student, studying a joint major in archaeology and economics in University College Dublin. His research interests include archaeogenetics, the economic history of the Bronze +and Iron age Mediterranean and archaeometallurgical studies. He is also interested in the use of digital technology as a means of communicating archaeological research with the general public