Guest blog: Ancient DNA and its applications to Ontario archaeology

Our latest Sustainable Archaeology: McMaster guest post is by research volunteer Chris Kendall, a fourth year Honours Anthropology student at McMaster University.

Ancient DNA and Its Applications to Ontario Archaeology

By: Chris Kendall, Honours Anthropology (IV), McMaster University

My role as a research volunteer at Sustainable Archaeology: McMaster, attempts to marry the molecular biological side of anthropology with its archaeological foundations. Over the course of the past semester, I have been examining the collections, working with staff and volunteers, and preparing a technical bulletin for the application of ancient DNA (aDNA) analysis in Ontario. While I was preparing this bulletin, I kept in mind the materials available in the collections, as well as some information researchers may need when beginning a project on aDNA analysis of Ontario archaeological finds. The technical bulletin outlines methodological frameworks on how to select ideal samples for aDNA analysis within the curated samples housed at the Sustainable Archaeology. From a genetics standpoint, many of the samples hold great potential for study. An abundance of faunal remains, combined with agricultural and botanical remains, hair, and sediment may be analyzed for aDNA material. 

The technical bulletin suggests proper storage techniques for organic samples in order to optimally preserve the genetic material. For example, fibres recovered from a water-logged site should be kept in ultra-pure water and not tap water since the chlorine can destroy any remaining DNA. This document can serve as a reference guide to both external researchers interested in using the collections, but also for the facility’s staff to ensure minimal damage and contamination occur to these specimens. It is hoped that from this technical bulletin more researchers will apply aDNA analysis to the study of the faunal and agricultural remains of Ontario. 

Of particular interest to me, is trying to better understand the evolutionary relationships of Ontario archaeological dog specimens. There are many dog skeletons currently in the collection, however, no phylogenetic relationships have been established for these groups, while other North American dog samples have been widely studied (Barta, 2007; Brown et al., 2012, for example). One study by Bathurst and Barta (2004) examined a dog with tuberculosis found at an Ontario Iroquois site, which is currently stored at Sustainable Archaeology: McMaster. Bathurst and Barta (2004) made inferences about human-canine interactions of these people based upon the genetic and skeletal markers, as well as the burial context of the animal. Further analysis of similar remains could look at domestication and migration patterns, which has rarely been studied in the context of Ontario archaeology sites. 

My time spent at the lab has been extremely beneficial. The collections are vast and exciting, so the ability to work so closely with them was a great opportunity. Working with the lab group has taught me a wide variety of skills I have found to be quite complementary to my academic life as both an undergraduate and hopeful graduate student. For instance, I learned that many other sources of DNA exist apart from tissue and skeletal remains. I also became aware of several rules of thumb for storing specimens I was not aware of before researching for this bulletin, such as storing items in humid conditions can lead to hydrolytic damage of the DNA. I also learned that differing techniques for isolating and extracting DNA can give varying results, as can cross-sectioning versus powdering a tooth or using cancellous instead of spongy bone.

Perhaps the most rewarding experience of all is being in contact with individuals with such a wide variety of research interests and schools of discipline. It is interesting to work with researchers, fellow undergraduates, and graduate students all dedicated to better understanding the past human experience of living in Ontario. In doing this, archaeologists work closely with ceramic experts, who collaborate with historians, museums, bioarchaeologists, and others. This blending of mutual interest creates a dynamic work and research environment that I am extremely grateful to be involved with.

References:

Barta, Jodi Lynn

2007     Addressing Issues of Domestication and Cultural Continuity on the Northwest Coast Using Ancient DNA and Dogs. PhD Dissertation, Department of Anthropology, McMaster University. 

Bathurst, Rhonda R. and Jodi Lynn Barta

2004     Molecular Evidence of Tuberculosis Induced Hypertrophic Osteopathy in a 16th Century Iroquoian Dog. Journal of Archaeological Science, 31: 917-925, doi:10.1016.j.jas.2003.12.006

Brown, Sarah K., Christyann M. Darwent, and Benjamin N. Sacks

2012     Ancient DNA Evidence for Genetic Continuity in Arctic Dogs. Journal of Archaeological Science xxx 1-10, doi: http://dx.doi.org/10.1016/j.jas.2012.09.010

Shelf Labeling

As part of our testing of the inventory management portion of the database, we've begun labeling our shelves here at SA: Western. With a capacity for over 54,000 boxes, and shelves that are 16 feet high, we needed a system that would allow us to quickly and easily identify, locate, retrieve, and re-shelve collections. Our labeling system must integrate with other inventory management aspects of the database, and had to be fool-proof - imagine trying to locate a single missing box that has been shelved in the wrong location out of the thousands around it!

To ensure that boxes are not easily misplaced, we developed a labeling system that incorporates barcode scanning rather than manual data entry. Our shelf labels include both a human readable version of the alphanumeric shelf address (for easy reference out in the shelves), as well as a 2 dimensional data matrix (DM) barcode. In order to remove or re-shelve boxes, the user scans the RFID tag that contains the unique name for that box (it's Box ID), opening the record for that box. The user then either selects to "remove" or disassociate that box from it's shelf, or, scans in the shelf DM code to associate the Box ID and shelf location.

To read more about Sustainable Archaeology's inventory management system, check out the last edition of our newsletter Notes from the SA.

Sustainable Archaeology: McMaster's Telecentric Microscope

Lena Zepf (pictured below) is a Masters student in the Department of Anthropology at McMaster University. Using Sustainable Archaeology: McMaster's telecentric microscope, Lena is examining smoking pipes from sites in Ontario.

Investigating cultural transformation in south-central Ontario: 

an examination of smoking pipes

My MA thesis investigates how smoking pipes change through time, and if certain changes to style can provide insight into cultural transformation in the context of shifting settlement strategies. The purpose of this investigation is two-fold, and consists of a visual and an attribute analysis of a series of sites in the Credit River watershed in Mississauga, and surrounding area. What I am looking for is evidence of style preferences and/or local stylistic changes. Sites of interest include the Wallace and Antrex sites (located at the University of Toronto in Mississauga), as well as the River and Chappell Terrace sites (found at the Peel Art Gallery Museum and Archives).

Sustainable Archaeology at McMaster Innovation Park has provided me with access to materials from some of the southern Ontario site collections as well access to a telecentric microscope, which has allowed me to observe ceramic tempers. Preliminary results, at this time, point towards site specific preferences in style, and in increase in pipe prevalence.

Digital Tools for Archaeological Collections and Inventory Management

Collections and inventory management strategies at Sustainable Archaeology: Western were presented at the 2013 Society for American Archaeology (SAA) annual meeting in Honolulu, Hawaii by Dr. Rhonda Bathurst and Kira Westby. The poster and its abstract can be viewed below. For more information on Sustainable Archaeology's inventory management strategies, check out the April/May edition of our newsletter Notes from the SA.

Poster Abstract: Digital Tools for Archaeological Collections and Inventory Management

What does archaeology have in common with weapons manufacturers, NASA or the automotive industry? All require a means of effectively managing and tracking inventory. There is a lot that archaeologists can borrow from the standards of practice implemented by these industries. Advances in coding and labeling systems such as 2D data matrix (DM) and radio-frequency identification (RFID) can speed up the process of data input and retrieval, alleviate transcription issues related to human error, minimize damage to artifacts, and automate collection tracking. Using DM codes to label and track individual artifacts and RFID tags to manage and track storage containers, this paper demonstrates a field-to-shelf solution for archaeological collections management utilizing some of the digital tools currently employed by major manufacturing industries.

Notes from the SA: April-May 2013

The April-May edition of Notes from the SA, Sustainable Archaeology: Western's newsletter. 

Micro-CT Scanning by the Art Gallery of Ontario

In the summer of 2012, Sustainable Archaeology worked with Art Gallery of Ontario (AGO) conservator Lisa Ellis and curator Sasha Suda to micro-CT scan 16th century prayer beads, in order to understand how these complex and intricately carved beads were constructed. Their work is the subject of  recent AGO Art Matters blog, titled "Conservation Notes: A very fine resolution". The project was also featured in the Spring 2013 CODART e-zine. The video below (posted on the AGO's Youtube channel) shows a surface rendered model of one of the prayer beads.  

This animation is a surface rendered model of the prayer bead, created from a 21 gigabyte, three-dimensional volume of micro-CT data, using VGStudio MAX. Animation created by Zoe Morris. Courtesy of Sustainable Archaeology: Western University, 2012. Prayer bead. Workshop of Adam Dirksz. 1500-1550. AGOID 29365. The Thomson Collection © Art Gallery of Ontario.

Guest Blog #5: Volunteering at Sustainable Archaeology: McMaster

Our fifth guest post was written by Julilla Paul, a third year Honours Anthropology student at McMaster University. She writes about her volunteer work at Sustainable Archaeology: McMaster, focusing on the processing, re-bagging, and analysis of coffin hardware from the St. Thomas Anglican Cemetery (Belleville, Ontario).

Volunteering at Sustainable Archaeology: McMaster 

By: Julilla Paul, Honours Anthropology (III), McMaster University

I discovered that Sustainable Archaeology at McMaster Innovation Park was going to open in this past summer, and the day I found out was the day I sent in an e-mail to ask if they were accepting student volunteers. The first thing that struck me as I entered the facility was its size. The facility is composed of a wet for processing samples and dry lab for high resolution microscopy as well as a massive storage area for archaeological collections. The storage area is a vast space lined with waiting shelves, each poised in anticipation of the arrival of archaeological material from across the province. I had spent part of the summer on an archaeological field school in Italy over the summer and I had even volunteered in a small anthropology lab before, however neither of these experiences prepared me for what awaited me in this new space. This lab was ripe with new opportunities to learn how materials from the field are processed, stored, and analyzed. Both the wet and dry labs sport an open layout, bright lights, and a general air of fresh excitement, an eagerness for what is to come. At least, that is how it is seen through the eyes of a starry-eyed student volunteer. After my inaugural tour of the facility, I was put to work building the standardized archival boxes.

Building boxes at the Sustainable Archaeology lab is a rite of passage and fulfills the practical necessity of furnishing its attached storage space. It acts as an introduction to the rhythms of the lab as well as its people and spaces. My first few weeks were spent building boxes to fill the shelves. However, short diversions from this introductory task were soon interspersed in my sessions. At first, I was introduced to the task of re-bagging artifacts for storage. All of the material coming into the facility must be re-bagged in archival grade, acid free bags and labelled based on a standardized system. My work began with the coffin hardware from the St. Thomas Anglican Cemetery sorting the decorative metal handles, rivets and nails that remained from the burials. 

Julilla working with collections in the McMaster lab

St. Thomas Anglican Cemetery was located in Belleville, Ontario and was used from 1821-1874 (McKillop, 1995). A total of 579 graves were excavated on the site in 1989 and yet it is estimated that this represents only 37% of the total number of graves present in the cemetery (McKillop, 1995). Coffin hardware on the site shows a high degree variability in style and form. While some of it was produced in the area, mass-produced coffin hardware emerged in the 19th century when the cemetery was still in use (McKillop, 1995).  

Coffin hardware from the St. Thomas Anglican Cemetery

Currently, we’re working on a pilot project using XRF to test the variability in the quality of metals used in the manufacture of the coffin hardware. This project captivated my attention because it added to my understanding of historic European burial practices and the process of understanding the archaeology of death. I have delved into the world of mortuary archaeology and what I see is fascinating. I am eager to see how the results of the analysis of coffin hardware compare to the previously conducted studies of the osteology of the individuals from this historic cemetery site. 

Brandi MacDonald using the hand-held XRF

Volunteering at a lab still in its infancy provides a multitude of opportunities for an interested student. I was introduced to a full spectrum of lab activities from building boxes to observing thin sectioning procedures. Other student research assistants and volunteers photograph artifacts, drill samples, and test standard operating procedures. These tasks have application both in research activities and the day to day needs of a lab. At Sustainable Archaeology, I’ve had the opportunity to work closely with other student research assistants and engage in areas of research that relate to my academic interests. In this vibrant atmosphere, I still leave the lab each day with the same fervent excitement that I brought with me on my tour five months ago.

Resources for additional information on the St. Thomas Anglican Cemetery Site:

Grauer, A. (Ed). (1995). Bodies of evidence: Reconstructing history through skeletal analysis. New York: Wiley-Liss Inc.

Herring, D., Saunders, S. R., and Katzenberg, M. A. (1998). Investigating the weaning process in past populations. American Journal of Physical Anthropology, 105(4), 425-439.

McKillop, H. (1995). Recognizing Children's Graves in Nineteenth-Century Cemeteries: Excavations in St. Thomas Anglican Churchyard, Belleville, Ontario, Canada. Historical Archaeology, 77-99.

Saunders, S., DeVito, C., Herring, A., Southern, R., and Hoppa, R. (1993). Accuracy tests of tooth formation age estimations for human skeletal remains. American Journal of Physical Anthropology, 92(2), 173-188.

Saunders, S., Hoppa, R., and Southern, R. (1993). Diaphyseal growth in a nineteenth century skeletal sample of subadults from St Thomas' Church, Belleville, Ontario. International Journal of Osteoarchaeology, 3(4), 265-281.