Thomas Royle

Simon Fraser University, Archaeology, Graduate Student

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I am interested in how ancient DNA (aDNA) analysis of archaeological and paleontological materials can be used to test and inform archaeological interpretations. Specifically, I am interested in how it can be used to address questions concerning the nature of palaeoenvironments, and the relationship between past human groups and their environments. Although I am interested in using aDNA analysis to study materials from any region, I am particularly interested in the archaeology of British Columbia’s Interior Plateau, Mesoamerica, and Ontario Mesoamerica.

My master’s research will use aDNA analysis to identify the species of salmon remains from EeRb-144, a large multi-component site (Early to Late Prehistoric Period) located in British Columbia’s Interior Plateau. By comparing the taxonomic composition of EeRb-144’s Middle and Late Period salmon assemblage, I hope to understand how salmon fishing strategies changed over time in the Interior Plateau.
Supervisors: Dongya Yang and George Nicholas
Address: Ancient DNA Laboratory
Department of Archaeology
Simon Fraser University
8888 University Drive
Burnaby, B.C. V5A 1S6

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University of York

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The University of Georgia

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Western University Canada

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Kansas State University

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Centro de Investigacion y Estudios Avanzados del IPN

Armando Marques-Guedes

UNL - New University of Lisbon

Enrico Cirelli

Università di Bologna

girolamo fiorentino

University of Salento

Ramiro Barberena

National Scientific and Technical Research Council

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Thesis by Thomas Royle

Ancient DNA Analysis of Middle and Late Period Archaeological Fish Remains from Kamloops, British Columbia

In this study, ancient DNA (aDNA) analysis was used to assign species identifications to a sample... more In this study, ancient DNA (aDNA) analysis was used to assign species identifications to a sample of Middle (7,000 to 4,500 years BP) and Late (4,500 to 200 years BP) Period fish remains from EeRb-144, a large campsite located in the Interior Plateau region of south-central British Columbia, Canada. The results of this analysis indicate that largescale sucker (Catostomus macrocheilus) (NISP=12) and northern pikeminnow (Ptychocheilus oregonensis) (NISP=8) are the most abundant species in the assemblage of Late Period fish remains from EeRb-144. This suggests these two taxa were the focus of the Late Period fishery at EeRb-144. Smaller quantities of peamouth chub (Mylocheilus caurinus) (NISP=3), longnose sucker (Catostomus catostomus) (NISP=1), and Chinook salmon (Oncorhynchus tshawytscha) (NISP=1) were also identified in the assemblage. Ecological data concerning the seasonal availability of these taxa and limited ethnographic accounts suggest EeRb-144’s Late Period fishery likely occurred during the spring and summer. The Middle Period fishery at the site also harvested largescale sucker (NISP=2), peamouth chub (NISP=1), and longnose sucker (NISP=1). These findings indicate locally abundant resident fish species were a potentially significant component of EeRb-144’s pre-contact fisheries, corroborating and refining the results of morphological faunal analyses from the area. In addition, the identification of largescale sucker, peamouth chub, and longnose sucker in both assemblages suggests there was some long-term continuity in fishing practices at the site.

This study demonstrates the feasibility of using ancient DNA analysis to identify fish remains from a variety of taxa to the species-level even when they lack taxonomically informative morphological features. The results also highlight that in order to improve aDNA analysis’ ability to discriminate between fish species there needs to be continued research into identifying useful DNA markers for species identification.

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Papers by Thomas Royle

Investigating the sex-selectivity of a Middle Ontario Iroquoian Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) fishery through ancient DNA analysis

by Thomas Royle, Eric Guiry, Suzanne Needs-Howarth, and Trevor Orchard

Journal of Archaeological Science: Reports, 2020

Prior to European settlement, Indigenous peoples sustainably harvested Atlantic salmon (Salmo sal... more Prior to European settlement, Indigenous peoples sustainably harvested Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) from Lake Ontario for centuries. Previous studies have suggested Indigenous peoples were able to maintain the productivity of Atlantic salmon and lake trout fisheries in the Great Lakes region through the use of resource management strategies. Since males tend to be the surplus sex among salmonids, one way in which Indigenous peoples could have managed Atlantic salmon and lake trout stocks was through the preferential harvesting of males. Here, we sought to investigate whether Indigenous peoples traditionally used sex-selective fishing to manage Lake Ontario Atlantic salmon and lake trout stocks. To address this question, we modified a DNA-based sex identification method developed for ancient Pacific salmonid (Oncorhynchus spp.) remains to make it applicable to archaeological Atlantic salmonid (Salmo spp.) and char (Salvelinus spp.) remains. This method assigns sex identities to samples through two PCR assays that co-amplify a fragment of the Y-specific salmonid master sex-determining gene (sexually dimorphic on the Y-chromosome gene) and an internal positive control, consisting of a fragment of the mitochondrial D-loop or nuclear clock1b gene. We applied this method to 61 Atlantic salmon and lake trout remains from the Antrex site (AjGv-38), a Middle Ontario Iroquoian (ca. CE 1250 to 1300) village located in the Lake Ontario watershed. Using this method, we successfully assigned sex identities to 51 of these remains (83.61% success rate), highlighting our method’s sensitivity and efficacy. Statistical analyses indicate neither the aggregate sex ratio nor the sex ratios obtained for the individual species were male-biased. This suggests Antrex’s Middle Ontario Iroquoian inhabitants probably did not practice male-selective fishing for Atlantic salmon or lake trout.

Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications

by Eric Guiry, Thomas Royle, Nicholas Waber, Thomas J Brown, and Bruce Finney

PLOS One, 2020

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy... more The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ 13 C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncor-hynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anad-romous and potamodromous ecotypes are broadly distinguishable on the basis of the δ 13 C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ 13 C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.

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Dietary plasticity and the extinction of the passenger pigeon (Ectopistes migratorius)

by Trevor Orchard, Thomas Royle, and Christina Cheung

Quaternary Science Reviews, 2020

The decline of passenger pigeons (Ectopistes migratorius) during the late nineteenth century cont... more The decline of passenger pigeons (Ectopistes migratorius) during the late nineteenth century continues to draw substantial public and scientific attention as perhaps the most (in-)famous extinction event in North America’s recent history. While humans undeniably caused the extinction, the relative importance of indirect (habitat destruction) versus direct (overhunting) impacts has remained a mystery, in part, due to a lack of scientific evidence for critical aspects of the species’ dietary ecology. One key factor in explaining why passenger pigeons went extinct is that their highly specialized diet and foraging strategy, focusing on mast (tree nuts), were no longer feasible as the forested habitats that they depended on became depleted by deforestation. We used stable isotope (d13C and d15N, n=94) and ancient DNA (n=9) analyses of archaeological specimens to demonstrate that, during the later Holocene, passenger pigeons had a substantial degree of dietary plasticity (including some individuals specializing in consumption of agricultural crops) that could have allowed them to take advantage of other food opportunities when mast became scarce. Dietary variation is not linked with either biological age (juveniles versus adults) or haplogroup. These results suggest that habitat destruction was less important for the passenger pigeon’s extinction than the impacts of hunting and trapping and highlight the tremendous potential of the archaeological record for exploring the factors that led to this species’ extinction.

An efficient and reliable DNA-based sex identification method for archaeological Pacific salmonid (Oncorhynchus spp.) remains

Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in... more Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently , little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region's Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay co-amplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method's reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method's reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method's sensitivity. The method's reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmo-nid remains.

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FISHING THROUGH TIME. Archaeoichthyology, Biodiversity, Ecology and Human Impact on Aquatic Environments. PROGRAM AND ABSTRACTS OF THE 18TH INTERNATIONAL COUNCIL FOR ARCHAEOZOOLOGY - FISH REMAINS WORKING GROUP.

TRABALHOS DO LARC, Sep 2015

In this volume of Trabalhos do LARC we present the Program and Abstracts of the 18th biennial mee... more In this volume of Trabalhos do LARC we present the Program and Abstracts of the 18th biennial meeting of
the International Council for Archaeozoology - Fish Remains Working Group (ICAZ-FRWG), hosted by the
Directorate-General for Cultural Heritage - Archaeosciences Laboratory (DGPC - LARC) and the Research
Centre in Biodiversity and Genetic Resources – Environmental Archaeology Research Group (CIBIO -
EnvArch).
The meeting is aimed primarily for archaeozoologists interested in the systematic study of fish bones
retrieved from archaeological sites around the world, and also to archaeologists, ichthyologists, historians,
ethnographers, and fishery biologists. To this end the conference is structured to encompass a multiplicity
of approaches to the study of fish remains and their contribution to our understanding of how fishing, fish
trade, fish consumption, biodiversity, ecology and human impact on aquatic environments have changed
through time.

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Ancient DNA Analysis of Middle and Late Period Archaeological Fish Remains from Kamloops, British Columbia

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Investigating the sex-selectivity of a Middle Ontario Iroquoian Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) fishery through ancient DNA analysis

by Thomas Royle, Eric Guiry, Suzanne Needs-Howarth, and Trevor Orchard

Journal of Archaeological Science: Reports, 2020