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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries. Sci Rep 2022; 12:13512. [PMID: 35933511 PMCID: PMC9357025 DOI: 10.1038/s41598-022-17656-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/28/2022] [Indexed: 11/08/2022] Open
Abstract
Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.
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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] [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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5
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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] [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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Andrews AJ, Puncher GN, Bernal-Casasola D, Di Natale A, Massari F, Onar V, Toker NY, Hanke A, Pavey SA, Savojardo C, Martelli PL, Casadio R, Cilli E, Morales-Muñiz A, Mantovani B, Tinti F, Cariani A. Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean. Sci Rep 2021; 11:20744. [PMID: 34671077 PMCID: PMC8528830 DOI: 10.1038/s41598-021-99708-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
| | - Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada.
| | - Darío Bernal-Casasola
- Department of History, Geography and Philosophy, Faculty of Philosophy and Letters, University of Cádiz, Cádiz, Spain
| | | | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Vedat Onar
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Nezir Yaşar Toker
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Alex Hanke
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | | | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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7
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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8
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Mobilizing the past to shape a better Anthropocene. Nat Ecol Evol 2021; 5:273-284. [PMID: 33462488 DOI: 10.1038/s41559-020-01361-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/08/2020] [Indexed: 01/29/2023]
Abstract
As our planet emerges into a new epoch in which humans dominate the Earth system, it is imperative that societies initiate a new phase of responsible environmental stewardship. Here we argue that information from the past has a valuable role to play in enhancing the sustainability and resilience of our societies. We highlight the ways that past data can be mobilized for a variety of efforts, from supporting conservation to increasing agricultural sustainability and food security. At a practical level, solutions from the past often do not require fossil fuels, can be locally run and managed, and have been tested over the long term. Past failures reveal non-viable solutions and expose vulnerabilities. To more effectively leverage increasing knowledge about the past, we advocate greater cross-disciplinary collaboration, systematic engagement with stakeholders and policymakers, and approaches that bring together the best of the past with the cutting-edge technologies and solutions of tomorrow.
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9
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Bas M, Salemme M, Green EJ, Santiago F, Speller C, Álvarez M, Briz I Godino I, Cardona L. Predicting habitat use by the Argentine hake Merluccius hubbsi in a warmer world: inferences from the Middle Holocene. Oecologia 2020; 193:461-474. [PMID: 32424465 DOI: 10.1007/s00442-020-04667-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 05/06/2020] [Indexed: 11/24/2022]
Abstract
Fish skeletal remains recovered from two archaeological sites dated in the Middle Holocene of Tierra del Fuego (Argentina) were analysed to describe habitat use patterns by hake in the past and predict changes in a warmer world. Mitochondrial DNA was successfully extracted and amplified from 42 out of 45 first vertebra from ancient hake and phylogenetic analysis assigned all haplotypes to Argentine hake (Merluccius hubbsi). According to osteometry, the Argentine hake recovered from the archaeological site were likely adults ranging 37.2-58.1 cm in standard length. C and N stable isotope analysis showed that currently Argentine hake use foraging grounds deeper than those of Patagonian blenny and pink cusk-eel. Argentine hake, however, had a much broader isotopic niche during the Middle Holocene, when a large part of the population foraged much shallower than contemporary pink cusk-eel. The overall evidence suggests the presence of large numbers of Argentine hake onshore Tierra del Fuego during the Middle Holocene, which allowed exploitation by hunter-gatherer-fisher groups devoid of fishing technology. Interestingly, average SST off Tierra del Fuego during the Middle Holocene was higher than currently (11 °C vs 7 °C) and matched SST in the current southernmost onshore spawning aggregations, at latitude 47 °S. This indicates that increasing SST resulting from global warming will likely result into an increased abundance of adult Argentine hake onshore Tierra del Fuego, as during the Middle Holocene. Furthermore, stable isotope ratios from mollusc shells confirmed a much higher marine primary productivity during the Middle Holocene off Tierra del Fuego.
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Affiliation(s)
- Maria Bas
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina. .,Department of Evolutionary Biology, Ecology and Environmental Science, Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain.
| | - Mónica Salemme
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina.,ICSE, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina
| | | | - Fernando Santiago
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
| | - Camilla Speller
- Department of Archaeology, BioArCh, University of York, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
| | - Myrian Álvarez
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
| | - Ivan Briz I Godino
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina.,Department of Archaeology, University of York, York, UK.,P. Rockefeller Visiting Scholar, DRCLAS at Harvard University, Cambridge, MA, USA
| | - Luis Cardona
- Department of Evolutionary Biology, Ecology and Environmental Science, Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
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10
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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] [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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11
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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12
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Kerr Q, Fuentes‐Pardo AP, Kho J, McDermid JL, Ruzzante DE. Temporal stability and assignment power of adaptively divergent genomic regions between herring ( Clupea harengus) seasonal spawning aggregations. Ecol Evol 2019; 9:500-510. [PMID: 30680131 PMCID: PMC6342187 DOI: 10.1002/ece3.4768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 11/07/2022] Open
Abstract
Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.
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Affiliation(s)
- Quentin Kerr
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | - James Kho
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jenni L. McDermid
- Marine Fish and Mammals Section, Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
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Rodrigues AT, McKechnie I, Yang DY. Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management. PLoS One 2018; 13:e0192716. [PMID: 29438388 PMCID: PMC5811035 DOI: 10.1371/journal.pone.0192716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 01/29/2018] [Indexed: 11/18/2022] Open
Abstract
Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.
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Affiliation(s)
- Antonia T. Rodrigues
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (ATR); (IM); (DYY)
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, British Columbia, Canada
- Hakai Institute, Heriot Bay, Quadra Island, British Columbia, Canada
- * E-mail: (ATR); (IM); (DYY)
| | - Dongya Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (ATR); (IM); (DYY)
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Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany. Proc Natl Acad Sci U S A 2017; 114:9152-9157. [PMID: 28784790 DOI: 10.1073/pnas.1710186114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.
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Bernaś R, Poćwierz-Kotus A, Dębowski P, Wenne R. The genetic relationship between extirpated and contemporary Atlantic salmon Salmo salar L. lines from the southern Baltic Sea. Genet Sel Evol 2016; 48:29. [PMID: 27038775 PMCID: PMC4818505 DOI: 10.1186/s12711-016-0208-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/22/2016] [Indexed: 12/03/2022] Open
Abstract
Background The genetic relationship between original Atlantic salmon populations that are now extinct in the southern Baltic Sea and the present-day populations has long been controversial. To investigate and clarify this issue, we successfully genotyped individuals of the historical populations from the Oder and Vistula Rivers using DNA extracted from dried scales with the Atlantic salmon single nucleotide polymorphism array. Results Our results showed a global FST of 0.2515 for all pairs of loci, which indicates a high level of genetic differentiation among the groups analyzed in this study. Pairwise FST values were significant for all comparisons and the highest values were found between present-day reintroduced Slupia River salmon and extinct Vistula River Atlantic salmon. Bayesian analysis of genetic structure revealed the existence of substructures in the extirpated Polish populations and three main clades among studied stocks. Conclusions The historical salmon population from the Oder River was genetically closer to present-day salmon from the Neman River than to the historical salmon from the Vistula River. Vistula salmon clearly separated from all other analyzed salmon stocks. It is likely that the origins of the Atlantic salmon population from the Morrum River and the Polish historical native populations are different. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0208-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafał Bernaś
- Department of Migratory Fishes, Inland Fisheries Institute, 83-330, Rutki, Żukowo, Poland.
| | | | - Piotr Dębowski
- Department of Migratory Fishes, Inland Fisheries Institute, 83-330, Rutki, Żukowo, Poland
| | - Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, 81-712, Sopot, Poland
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Ruggeri P, Splendiani A, Di Muri C, Fioravanti T, Santojanni A, Leonori I, De Felice A, Biagiotti I, Carpi P, Arneri E, Nisi Cerioni P, Giovannotti M, Caputo Barucchi V. Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus). PLoS One 2016; 11:e0151507. [PMID: 26982808 PMCID: PMC4794184 DOI: 10.1371/journal.pone.0151507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/29/2016] [Indexed: 11/18/2022] Open
Abstract
It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (Ne) are much smaller than those expected in a fishes with large population census sizes (Nc). Estimates of Ne indicate low effective population sizes, even before the population collapse. The ratio Ne/Ne ranged between 10-6 and 10-8, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.
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Affiliation(s)
- Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cristina Di Muri
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alberto Santojanni
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Iole Leonori
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Andrea De Felice
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Ilaria Biagiotti
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Piera Carpi
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
| | - Enrico Arneri
- FAO-FIRF, Fisheries and Aquaculture Department, AdriaMed Project, Viale delle Terme di Caracalla, 00153 Roma, Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima, Largo Fiera della Pesca, 60125 Ancona, Italy
- * E-mail:
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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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Speller C, Kooyman B, Rodrigues A, Langemann E, Jobin R, Yang D. Assessing prehistoric genetic structure and diversity of North American elk ( Cervus elaphus) populations in Alberta, Canada. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
North American elk (Cervus elaphus L., 1758) are an important component of Canada’s natural ecosystems. Overhunting and habitat decline in the 19th century led to the near eradication of Rocky Mountain elk (Cervus elaphus nelsoni Bailey, 1935) and Manitoban elk (Cervus elaphus manitobensis Millais, 1915) within Alberta. Though elk populations have been restored within provincial and national parks, it is unknown to what degree historic population declines affected overall genetic diversity and population structuring of the two subspecies. This study targeted 551 bp of mitochondrial D-loop DNA from 50 elk remains recovered from 16 archaeological sites (2260 BCE (before common era) to 1920 CE (common era)) to examine the former genetic diversity and population structure of Alberta’s historic elk populations. Comparisons of ancient and modern haplotype and nucleotide diversity suggest that historic population declines reduced the mitochondrial diversity of Manitoban elk, while translocation of animals from Yellowstone National Park in the early 20th century served to maintain the diversity of Rocky Mountain populations. Gene flow between the two subspecies was significantly higher in the past than today, suggesting that the two subspecies previously formed a continuous population. These data on precontact genetic diversity and gene flow in Alberta elk provide essential baseline data integral for elk management and conservation in the province.
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Affiliation(s)
- C.F. Speller
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - B. Kooyman
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - A.T. Rodrigues
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - E.G. Langemann
- Cultural Resource Services, Western and Northern Service Centre, Parks Canada, Calgary, AB T2P 3M3, Canada
| | - R.M. Jobin
- Special Investigations and Forensic Services Section, Fish and Wildlife Enforcement Branch, Justice and Solicitor General, Government of Alberta, 7th Floor, OS Longman Building, 6909-116 Street, Edmonton, AB T6H 4P2, Canada
| | - D.Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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