Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

Anne Katharine Runge; Jessica Hendy; Kristine Richter; Edouard Masson-MacLean; Kate Britton; Meaghan Mackie; Krista McGrath; Matthew Collins; Enrico Cappellini; Camilla Speller

doi:10.1098/rspb.2021.0020

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

Anne Katharine Runge^* (Corresponding Author), Jessica Hendy, Kristine Richter, Edouard Masson-MacLean, Kate Britton, Meaghan Mackie, Krista McGrath, Matthew Collins, Enrico Cappellini, Camilla Speller^* (Corresponding Author)

^*Corresponding author for this work

Archaeology

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Abstract

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed diet- ary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spec- trometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunal- leq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Original language	English
Article number	20210020
Number of pages	10
Journal	Proceedings of the Royal Society B: Biological Sciences
Volume	288
Issue number	1954
DOIs	https://doi.org/10.1098/rspb.2021.0020
Publication status	Published - 7 Jul 2021

Bibliographical note

Funding. This project has received funding from the European Union’s EU Framework Programme for Research and Innovation Horizon 2020 under Grant Agreement no. 676154 and the Danish National Research Foundation award PROTEIOS (DNRF128). The onsite col- lection of samples was carried out by staff and students from the University of Aberdeen, volunteer excavators and the residents of Quinhagak. Fieldwork/primary sampling was funded by an AHRC (AH/K006029/1) grant awarded to Rick Knecht (Aberdeen), K.B. and Charlotta Hillerdal (Aberdeen) and an AHRC-LabEx award (AH/N504543/1) to K.B., Rick Knecht (Aberdeen), Keith Dobney (Liverpool) and Isabelle Sidéra (Nanterre). We had logistical and planning support for fieldwork by Qanirtuuq Incorporated, Quinha- gak, Alaska, and the people of Quinhagak, who we also thank for sampling permissions. We thank Prof. Jesper Velgaard Olsen at the Novo Nordisk Center for Protein Research for providing access and resources, which was also funded in part by a donation from the Novo Nordisk Foundation (grant no. NNF14CC0001). Additional support was provided through the New Frontiers in Research grant no. (SSHRC NFRFE-2018-00066).

Acknowledgements. We further acknowledge Takumi Tsutaya for valu- able insight in implementing the protein extraction protocol and subsequent discussions, and Samantha Preslee for completing the ZooMS extractions and MALDI-TOF analysis in conjunction with the Technology Facility at the University of York. We are grateful to our three anonymous referees for their constructive comments and suggestions on our original manuscript.
8

Keywords

dogs
paleofaeces
palaeoproteomics
zooms
Alaska
archaeology
Nunalleq

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Runge, A. K., Hendy, J., Richter, K., Masson-MacLean, E., Britton, K., Mackie, M., McGrath, K., Collins, M., Cappellini, E., & Speller, C. (2021). Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome. Proceedings of the Royal Society B: Biological Sciences, 288(1954), Article 20210020. https://doi.org/10.1098/rspb.2021.0020

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abstract = "The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed diet- ary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spec- trometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunal- leq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.",

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author = "Runge, {Anne Katharine} and Jessica Hendy and Kristine Richter and Edouard Masson-MacLean and Kate Britton and Meaghan Mackie and Krista McGrath and Matthew Collins and Enrico Cappellini and Camilla Speller",

note = "Funding. This project has received funding from the European Union{\textquoteright}s EU Framework Programme for Research and Innovation Horizon 2020 under Grant Agreement no. 676154 and the Danish National Research Foundation award PROTEIOS (DNRF128). The onsite col- lection of samples was carried out by staff and students from the University of Aberdeen, volunteer excavators and the residents of Quinhagak. Fieldwork/primary sampling was funded by an AHRC (AH/K006029/1) grant awarded to Rick Knecht (Aberdeen), K.B. and Charlotta Hillerdal (Aberdeen) and an AHRC-LabEx award (AH/N504543/1) to K.B., Rick Knecht (Aberdeen), Keith Dobney (Liverpool) and Isabelle Sid{\'e}ra (Nanterre). We had logistical and planning support for fieldwork by Qanirtuuq Incorporated, Quinha- gak, Alaska, and the people of Quinhagak, who we also thank for sampling permissions. We thank Prof. Jesper Velgaard Olsen at the Novo Nordisk Center for Protein Research for providing access and resources, which was also funded in part by a donation from the Novo Nordisk Foundation (grant no. NNF14CC0001). Additional support was provided through the New Frontiers in Research grant no. (SSHRC NFRFE-2018-00066). Acknowledgements. We further acknowledge Takumi Tsutaya for valu- able insight in implementing the protein extraction protocol and subsequent discussions, and Samantha Preslee for completing the ZooMS extractions and MALDI-TOF analysis in conjunction with the Technology Facility at the University of York. We are grateful to our three anonymous referees for their constructive comments and suggestions on our original manuscript. 8",

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T1 - Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

AU - Runge, Anne Katharine

AU - Hendy, Jessica

AU - Richter, Kristine

AU - Masson-MacLean, Edouard

AU - Britton, Kate

AU - Mackie, Meaghan

AU - McGrath, Krista

AU - Collins, Matthew

AU - Cappellini, Enrico

AU - Speller, Camilla

N1 - Funding. This project has received funding from the European Union’s EU Framework Programme for Research and Innovation Horizon 2020 under Grant Agreement no. 676154 and the Danish National Research Foundation award PROTEIOS (DNRF128). The onsite col- lection of samples was carried out by staff and students from the University of Aberdeen, volunteer excavators and the residents of Quinhagak. Fieldwork/primary sampling was funded by an AHRC (AH/K006029/1) grant awarded to Rick Knecht (Aberdeen), K.B. and Charlotta Hillerdal (Aberdeen) and an AHRC-LabEx award (AH/N504543/1) to K.B., Rick Knecht (Aberdeen), Keith Dobney (Liverpool) and Isabelle Sidéra (Nanterre). We had logistical and planning support for fieldwork by Qanirtuuq Incorporated, Quinha- gak, Alaska, and the people of Quinhagak, who we also thank for sampling permissions. We thank Prof. Jesper Velgaard Olsen at the Novo Nordisk Center for Protein Research for providing access and resources, which was also funded in part by a donation from the Novo Nordisk Foundation (grant no. NNF14CC0001). Additional support was provided through the New Frontiers in Research grant no. (SSHRC NFRFE-2018-00066). Acknowledgements. We further acknowledge Takumi Tsutaya for valu- able insight in implementing the protein extraction protocol and subsequent discussions, and Samantha Preslee for completing the ZooMS extractions and MALDI-TOF analysis in conjunction with the Technology Facility at the University of York. We are grateful to our three anonymous referees for their constructive comments and suggestions on our original manuscript. 8

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N2 - The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed diet- ary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spec- trometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunal- leq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

AB - The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed diet- ary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spec- trometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunal- leq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

KW - dogs

KW - paleofaeces

KW - palaeoproteomics

KW - zooms

KW - Alaska

KW - archaeology

KW - Nunalleq

U2 - 10.1098/rspb.2021.0020

DO - 10.1098/rspb.2021.0020

M3 - Article

SN - 0962-8452

VL - 288

JO - Proceedings of the Royal Society B: Biological Sciences

JF - Proceedings of the Royal Society B: Biological Sciences

IS - 1954

M1 - 20210020

ER -

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

Abstract

Bibliographical note

Keywords

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