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Royle TCA, Guiry EJ, Zhang H, Clark LT, Missal SM, Rabinow SA, James M, Yang DY. Documenting the
short‐tailed
albatross (
Phoebastria albatrus
) clades historically present in British Columbia, Canada, through ancient
DNA
analysis of archaeological specimens. Ecol Evol 2022; 12:e9116. [PMID: 35923939 PMCID: PMC9339763 DOI: 10.1002/ece3.9116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
The short‐tailed albatross (Phoebastria albatrus) is a threatened seabird whose present‐day range encompasses much of the North Pacific. Within this species, there are two genetic clades (Clades 1 and 2) that have distinctive morphologies and foraging ecologies. Due to a global population collapse in the late 19th and early 20th centuries, the frequency of these clades among the short‐tailed albatross population that historically foraged off British Columbia, Canada, is unclear. To document the species' historical genetic structure in British Columbia, we applied ancient DNA (aDNA) analysis to 51 archaeological short‐tailed albatross specimens from the Yuquot site (Borden site number: DjSp‐1) that span the past four millennia. We obtained a 141 bp cytochrome b sequence from 43 of the 51 (84.3%) analyzed specimens. Analyses of these sequences indicate 40 of the specimens belong to Clade 1, while 2 belong to Clade 2. We also identified a single specimen with a novel cytochrome b haplotype. Our results indicate that during the past four millennia most of the short‐tailed albatrosses foraging near Yuquot belonged to Clade 1, while individuals from other lineages made more limited use of the area. Comparisons with the results of previous aDNA analyses of archaeological albatrosses from Japanese sites suggest the distribution of Clades 1 and 2 differed. While both albatross clades foraged extensively in the Northwest Pacific, Clade 1 albatrosses appear to have foraged along the west coast of Vancouver Island to a greater extent. Due to their differing distributions, these clades may be exposed to different threats.
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Affiliation(s)
- Thomas C. A. Royle
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
| | - Eric. J. Guiry
- School of Archaeology and Ancient History University of Leicester Leicester UK
- Department of Anthropology Trent University Peterborough Ontario Canada
- Department of Anthropology University of British Columbia Vancouver British Columbia Canada
| | - Hua Zhang
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
| | - Lauren T. Clark
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
| | - Shalegh M. Missal
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
| | - Sophie A. Rabinow
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
- Department of Archaeology University of Cambridge Cambridge UK
| | - Margaretta James
- Land of Maquinna Cultural Society Mowachaht/Muchalaht First Nation Tsaxana (Gold River) British Columbia Canada
| | - Dongya Y. Yang
- Ancient DNA Laboratory, Department of Archaeology Simon Fraser University Burnaby British Columbia Canada
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Morin J, Royle TCA, Zhang H, Speller C, Alcaide M, Morin R, Ritchie M, Cannon A, George M, George M, Yang D. Indigenous sex-selective salmon harvesting demonstrates pre-contact marine resource management in Burrard Inlet, British Columbia, Canada. Sci Rep 2021; 11:21160. [PMID: 34759290 PMCID: PMC8581006 DOI: 10.1038/s41598-021-00154-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
To gain insight into pre-contact Coast Salish fishing practices, we used new palaeogenetic analytical techniques to assign sex identifications to salmonid bones from four archaeological sites in Burrard Inlet (Tsleil-Waut), British Columbia, Canada, dating between about 2300-1000 BP (ca. 400 BCE-CE 1200). Our results indicate that male chum salmon (Oncorhynchus keta) were preferentially targeted at two of the four sampled archaeological sites. Because a single male salmon can mate with several females, selectively harvesting male salmon can increase a fishery's maximum sustainable harvest. We suggest such selective harvesting of visually distinctive male spawning chum salmon was a common practice, most effectively undertaken at wooden weirs spanning small salmon rivers and streams. We argue that this selective harvesting of males is indicative of an ancient and probably geographically widespread practice for ensuring sustainable salmon populations. The archaeological data presented here confirms earlier ethnographic accounts describing the selective harvest of male salmon.
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Affiliation(s)
- Jesse Morin
- grid.17091.3e0000 0001 2288 9830Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC Canada
| | - Thomas C. A. Royle
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
| | - Hua Zhang
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
| | - Camilla Speller
- grid.17091.3e0000 0001 2288 9830Department of Anthropology, University of British Columbia, Vancouver, BC Canada
| | - Miguel Alcaide
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada
| | - Ryan Morin
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada
| | - Morgan Ritchie
- grid.17091.3e0000 0001 2288 9830Department of Anthropology, University of British Columbia, Vancouver, BC Canada
| | - Aubrey Cannon
- grid.25073.330000 0004 1936 8227Department of Anthropology, McMaster University, Hamilton, ON Canada
| | | | | | - Dongya Yang
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
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Guiry E, Royle TCA, Matson RG, Ward H, Weir T, Waber N, Brown TJ, Hunt BPV, Price MHH, Finney BP, Kaeriyama M, Qin Y, Yang DY, Szpak P. Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications. PLoS One 2020; 15:e0232180. [PMID: 32343728 PMCID: PMC7188214 DOI: 10.1371/journal.pone.0232180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/08/2020] [Indexed: 02/02/2023] Open
Abstract
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 (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus 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 anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C 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 δ13C 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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Affiliation(s)
- Eric Guiry
- Department of Anthropology, Trent University, Peterborough, Ontario, Canada
- School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas C. A. Royle
- Department of Archaeology, Ancient DNA Laboratory, Simon Fraser University, Burnaby, British Columbia, Canada
| | - R. G. Matson
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hillary Ward
- Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Penticton, British Columbia, Canada
| | - Tyler Weir
- Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Penticton, British Columbia, Canada
| | - Nicholas Waber
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas J. Brown
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian P. V. Hunt
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Michael H. H. Price
- Department of Biological Sciences, Earth to Ocean Research Group, Simon Fraser University, British Columbia, Canada
| | - Bruce P. Finney
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
- Department of Geosciences, Idaho State University, Pocatello, Idaho, United States of America
| | | | - Yuxue Qin
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, Liaoning, China
| | - Dongya Y. Yang
- Department of Archaeology, Ancient DNA Laboratory, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, Ontario, Canada
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Royle TCA, Sakhrani D, Speller CF, Butler VL, Devlin RH, Cannon A, Yang DY. An efficient and reliable DNA-based sex identification method for archaeological Pacific salmonid (Oncorhynchus spp.) remains. PLoS One 2018. [PMID: 29538397 PMCID: PMC5851554 DOI: 10.1371/journal.pone.0193212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
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 salmonid remains.
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Affiliation(s)
- Thomas C. A. Royle
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (TCAR); (DYY)
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - Camilla F. Speller
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Virginia L. Butler
- Department of Anthropology, Portland State University, Portland, Oregon, United States of America
| | - Robert H. Devlin
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - Aubrey Cannon
- Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Dongya Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (TCAR); (DYY)
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