1
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Bringloe TT, Parent GJ. Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species. BMC Genomics 2023; 24:693. [PMID: 37985969 PMCID: PMC10659057 DOI: 10.1186/s12864-023-09779-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies. RESULTS The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2-3.7% of the total genome depending on the pairwise comparison of references. In addition, unsupported higher order scaffolding was identified in published reference genomes. In contrast, we estimated 8.2% of the compared narwhal genomes featured discrepancies, with inversions being notably abundant (5.3%). Discrepancies were linked to repetitive elements in both species. CONCLUSIONS We provide several new reference genomes for beluga (Delphinapterus leucas), while highlighting potential avenues for improvements. In particular, additional layers of data providing information on ultra-long genomic distances are needed to resolve persistent errors in reference genome construction. The comparative analyses of monodontid reference genomes suggested that the three new reference genomes for beluga are more accurate compared to the currently published reference genome, but that the new narwhal genome is less accurate than one published. We also present a conceptual summary for improving the accuracy of reference genomes with relevance to end-user needs and how they relate to levels of assembly quality and uncertainty.
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Affiliation(s)
- Trevor T Bringloe
- Laboratory of Genomics, Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, QC, Canada.
| | - Geneviève J Parent
- Laboratory of Genomics, Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, QC, Canada.
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2
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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3
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Rey-Iglesia A, Wilson T, Routledge J, Skovrind M, Garde E, Heide-Jørgensen MP, Szpak P, Lorenzen ED. Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2023; 59:66-77. [PMID: 36445837 DOI: 10.1080/10256016.2022.2145285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Stable carbon (δ13C) and nitrogen (δ15N) isotopic compositions of bone and dentine collagen extracted from museum specimens have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values need to be transformed into bone-collagen equivalent using a correction factor to allow comparisons between the two collagen sources. Here, we provide correction factors to transform dentine δ13C and δ15N values into bone-collagen equivalent for two toothed whales: narwhal and beluga. We sampled bone and dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in belugas, dentine was sampled from tooth. δ13C and δ15N were measured, and intra-individual bone and dentine isotopic compositions were used to calculate correction factors for each species. We detected differences in δ13C and δ15N. In both narwhals and belugas, we found lower average δ13C and δ15N in bone compared with dentine. The correction factors provided by the study enable the combined analysis of stable isotope data from bone and dentine in these species.
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Affiliation(s)
| | | | | | - Mikkel Skovrind
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eva Garde
- Greenland Institute of Natural Resources, Copenhagen, Denmark
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4
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Schroeder L, Ackermann RR. Moving beyond the adaptationist paradigm for human evolution, and why it matters. J Hum Evol 2023; 174:103296. [PMID: 36527977 DOI: 10.1016/j.jhevol.2022.103296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022]
Abstract
The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.
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Affiliation(s)
- Lauren Schroeder
- Department of Anthropology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada; Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa.
| | - Rebecca Rogers Ackermann
- Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa; Department of Archaeology, University of Cape Town, Rondebosch, 7701, South Africa.
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5
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Skull ecomorphological variation of narwhals (Monodon monoceros, Linnaeus 1758) and belugas (Delphinapterus leucas, Pallas 1776) reveals phenotype of their hybrids. PLoS One 2022; 17:e0273122. [PMID: 35960760 PMCID: PMC9374245 DOI: 10.1371/journal.pone.0273122] [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: 03/21/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Narwhals and belugas are toothed whales belonging to the Monodontidae. Belugas have a circumpolar Arctic and sub-Artic distribution while narwhals are restricted to the Atlantic Arctic. Their geographical ranges overlap during winter migrations in the Baffin Bay area (Canada/West Greenland) and successful interbreeding may occur. Here, we employed geometric morphometrics on museum specimens to explore the cranium and mandible morphology of a known hybrid (NHMD MCE 1356) and the cranium morphology of a putative hybrid (NHMD 1963.44.1.4) relative to skull morphological variation in the parental species. Specifically, we used 3D models of skulls from 69 belugas, 86 narwhals, and the two known/putative hybrids and 2D left hemi-mandibles from 20 belugas, 64 narwhals and the known hybrid. Skull shape analyses allowed clear discrimination between species. Narwhals are characterised by a relatively short rostrum and wide neurocranium while belugas show a more elongated and narrower cranium. Sexual size dimorphism was detected in narwhals, with males larger than females, but no sexual shape dimorphism was detected in either species (excluding presence/absence of tusks in narwhals). Morphological skull variation was also dependent on different allometric slopes between species and sexes in narwhals. Our analyses showed that the cranium of the known hybrid was phenotypically close to belugas but its 2D hemi-mandible had a narwhal shape and size morphology. Both cranium and mandible were strongly correlated, with the pattern of covariation being similar to belugas. The putative hybrid was a pure male narwhal with extruded teeth. Comparison of genomic DNA supported this result, and stable carbon and nitrogen isotope values suggested that the putative hybrid had a more benthic foraging strategy compared to narwhals. This work demonstrates that although the known hybrid could be discriminated from narwhals and belugas, detection of its affinities with these parental species was dependent on the part of the skull analysed.
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6
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Cabrera AA, Rey-Iglesia A, Louis M, Skovrind M, Westbury MV, Lorenzen ED. How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes. Ecol Evol 2022; 12:e9185. [PMID: 36035270 PMCID: PMC9405501 DOI: 10.1002/ece3.9185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex‐identification pipeline, for very low‐coverage shotgun sequencing data from a single individual. SeXY was designed to utilize low‐effort screening data for sex identification and does not require a conspecific sex‐chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high‐quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower‐quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.
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Affiliation(s)
| | | | - Marie Louis
- Globe Institute University of Copenhagen Copenhagen K Denmark.,Greenland Institute of Natural Resources Nuuk Greenland
| | - Mikkel Skovrind
- Globe Institute University of Copenhagen Copenhagen K Denmark
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7
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Faria DM, Steel D, Baker CS, da Silva JM, de Meirelles ACO, Souto LRA, Siciliano S, Barbosa LA, Secchi E, Di Tullio JC, de Oliveira LR, Ott PH, Farro APC. Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean. PLoS One 2022; 17:e0270690. [PMID: 35834534 PMCID: PMC9282552 DOI: 10.1371/journal.pone.0270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.
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Affiliation(s)
- Drienne Messa Faria
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
- * E-mail:
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - C. Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - José Martins da Silva
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Fernando de Noronha, PE, Brazil
| | | | | | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Eduardo Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Juliana Couto Di Tullio
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | | | - Paulo Henrique Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, RS, Brazil
- Universidade Estadual do Rio Grande do Sul (Uergs), Osório, RS, Brazil
| | - Ana Paula Cazerta Farro
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
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8
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Liu X, Schjøtt SR, Granquist SM, Rosing-Asvid A, Dietz R, Teilmann J, Galatius A, Cammen K, O Corry-Crowe G, Harding K, Härkönen T, Hall A, Carroll EL, Kobayashi Y, Hammill M, Stenson G, Frie AK, Lydersen C, Kovacs KM, Andersen LW, Hoffman JI, Goodman SJ, Vieira FG, Heller R, Moltke I, Tange Olsen M. Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Mol Ecol 2022; 31:1682-1699. [PMID: 35068013 PMCID: PMC9306526 DOI: 10.1111/mec.16365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.
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Affiliation(s)
- Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | | | - Sandra M Granquist
- Icelandic Seal Centre, Höfðabraut 6, 530, Hvammstangi, Iceland.,Marine and Freshwater Research Institute, Institute of Freshwater Fisheries Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - Rune Dietz
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jonas Teilmann
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | | | - Greg O Corry-Crowe
- Wildlife Evolution and Behavior Program, Florida Atlantic University, USA
| | - Karin Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, UK, KY16 8LB
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Yumi Kobayashi
- Laboratory of Animal Ecology, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Mike Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, QC, Canada
| | - Garry Stenson
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5667, St. John's NL, Canada
| | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Filipe G Vieira
- Center for Genomic Medicine, Copenhagen University Hospitalet, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Denmark
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9
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Inamori D, Kita YF, Funasaka N. External Morphological and Molecular Evidence of Natural Intrageneric Hybridization between Common and Indo-Pacific Bottlenose Dolphins (Tursiops truncatus × T. aduncus) from Japanese Waters. MAMMAL STUDY 2021. [DOI: 10.3106/ms2021-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daiki Inamori
- Taiji Whale Museum, Taiji, Higashimuro, Wakayama 649-5171, Japan
| | - Yuki F. Kita
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-ku, Sapporo, Hokkaido 005-8601, Japan
| | - Noriko Funasaka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, Kurimamachiya, Tsu, Mie 514-8507, Japan
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10
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Viehberg FA, Medeiros AS, Plessen B, Wang X, Muir D, Pienitz R. The influence of a lost society, the Sadlermiut, on the environment in the Canadian Arctic. Sci Rep 2021; 11:18504. [PMID: 34531423 PMCID: PMC8446097 DOI: 10.1038/s41598-021-97631-7] [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: 04/05/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
High latitude freshwater ecosystems are sentinels of human activity and environmental change. The lakes and ponds that characterize Arctic landscapes have a low resilience to buffer variability in climate, especially with increasing global anthropogenic stressors in recent decades. Here, we show that a small freshwater pond in proximity of the archaeological site “Native Point” on Southampton Island (Nunavut, Arctic Canada) is a highly sensitive environmental recorder. The sediment analyses allowed for pinpointing the first arrival of Sadlermiut culture at Native Point to ~ 1250 CE, followed by a dietary shift likely in response to the onset of cooling in the region ~ 1400 CE. The influence of the Sadlermiut on the environment persisted long after the last of their population perished in 1903. Presently, the pond remains a distorted ecosystem that has experienced fundamental shifts in the benthic invertebrate assemblages and accumulated anthropogenic metals in the sediment. Our multi-proxy paleolimnological investigation using geochemical and biological indicators emphasizes that direct and indirect anthropogenic impacts have long-term environmental implications on high latitude ecosystems.
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Affiliation(s)
- Finn A Viehberg
- Laboratoire de Paléoécologie Aquatique, Centre d'Études Nordiques, Pavillon Abitibi-Price, Université Laval, Québec, G1V 0A6, Canada. .,Institut Für Geographie Und Geologie, University of Greifswald, Friedrich-Ludwig-Jahn Str. 16, 17487, Greifswald, Germany.
| | - Andrew S Medeiros
- School for Resource and Environmental Studies, Dalhousie University, Halifax, B3H 4R2, Canada
| | - Birgit Plessen
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Climate Dynamics and Landscape Evolution, 14473, Potsdam, Germany
| | - Xiaowa Wang
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, L7S 1A1, Canada
| | - Derek Muir
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, L7S 1A1, Canada
| | - Reinhard Pienitz
- Laboratoire de Paléoécologie Aquatique, Centre d'Études Nordiques, Pavillon Abitibi-Price, Université Laval, Québec, G1V 0A6, Canada
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11
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Louis M, Skovrind M, Garde E, Heide-Jørgensen MP, Szpak P, Lorenzen ED. Population-specific sex and size variation in long-term foraging ecology of belugas and narwhals. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202226. [PMID: 33972883 PMCID: PMC8074634 DOI: 10.1098/rsos.202226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Intraspecific variation in resource use by individuals of different age, sex or size may reflect differing energetic requirements and physiological constraints. Males and females often show differences in diet owing to sexual size dimorphism, different life histories and/or habitat use. Here, we investigate how sex and size influence the long-term foraging ecology of belugas and narwhals in Greenland, using stable isotopes of carbon and nitrogen from bone collagen. We show that males have a higher trophic level and a larger ecological niche than females in West Greenland belugas and in East Greenland narwhals. In addition, for these two populations, we find that δ 15N increases with size, particularly in males. We hypothesize that sexual size dimorphism together with strong maternal investment drive these differences. By contrast, we find no differences in foraging ecology between sexes in West Greenland narwhals and observe no influence of size on trophic level. This may reflect the influence of interspecific competition in West Greenland, where the distributions of belugas and narwhals overlap, and/or geographical resource partitioning among different summer aggregations of narwhals. Our results suggest that sex and size variations in diet are population dependent, and probably the result of varying ecological interactions.
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Affiliation(s)
- Marie Louis
- Globe Institute, University of Copenhagen, Denmark
| | | | - Eva Garde
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | | | - Paul Szpak
- Trent University, Peterborough, Ontario, Canada
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12
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Guiry EJ, Hunt BPV. Integrating fish scale and bone isotopic compositions for 'deep time' retrospective studies. MARINE ENVIRONMENTAL RESEARCH 2020; 160:104982. [PMID: 32907720 DOI: 10.1016/j.marenvres.2020.104982] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Isotopic studies of archived fish scales have tremendous potential to develop long-term retrospectives that provide important insights into how humans have altered aquatic ecosystems. However, fish specimens in museum archives and other repositories typically date to time periods when the impacts of industrial societies may have already caused profound environmental changes. Archaeological fish bones offer an opportunity to bridge this key temporal gap by providing samples spanning from the recent past to as far back as the Pleistocene. Collagen is the primary protein component of both fish scale and bone, but the comparability of isotopic compositions from these tissues has not been established experimentally. To lay the framework for integrating isotopic datasets from these tissues, we compare δ13C and δ15N of bone and scale collagen, as well as other tissues, from fish with life-time controlled diets. Results show that while there is no difference in δ13C between scale and bone collagen, there may be a very slight but meaningful inter-tissue offset in δ15N (<0.3‰). We discuss potential sources of δ15N variation in scale and bone collagen measurements. Because there is no difference in scale and bone δ13C, and the observed offset in δ15N is very small (less than analytical uncertainty in many studies), our findings demonstrate that collagen isotopic compositions from these tissues should be directly comparable when integrating datasets from modern and ancient samples to build more powerful, millennium-scale isotopic times series. In linking isotopic compositions of collagen from modern, historical (scales), and archaeological (bones) fish, our findings open the way for more nuanced contextualization of how ecosystems functioned prior to large-scale exploitation and how they have responded to mounting anthropogenic pressures in the intervening centuries.
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Affiliation(s)
- Eric J Guiry
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE17RH, UK; Department of Anthropology, University of British Columbia, 6306 NW Marine Drive, Vancouver, BC, V6T 1Z1, Canada.
| | - Brian P V Hunt
- Institute for the Oceans and Fisheries, University of British Columbia, Aquatic Ecosystems Research Laboratory, 2202 Main Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2020 - 2207 Main Mall, Vancouver, BC, V6T 1Z4, Canada; Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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Guiry EJ, Szpak P. Quality control for modern bone collagen stable carbon and nitrogen isotope measurements. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13433] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric J. Guiry
- Department of Anthropology Trent University Peterborough ON Canada
- School of Archaeology and Ancient History University of Leicester Leicester UK
| | - Paul Szpak
- Department of Anthropology Trent University Peterborough ON Canada
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14
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Species assignment in forensics and the challenge of hybrids. Forensic Sci Int Genet 2020; 48:102333. [PMID: 32615399 DOI: 10.1016/j.fsigen.2020.102333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 01/04/2023]
Abstract
Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.
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Allen R, Ryan H, Davis BW, King C, Frantz L, Irving-Pease E, Barnett R, Linderholm A, Loog L, Haile J, Lebrasseur O, White M, Kitchener AC, Murphy WJ, Larson G. A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc Biol Sci 2020; 287:20200690. [PMID: 32486979 PMCID: PMC7341909 DOI: 10.1098/rspb.2020.0690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F1 hybrids are able to produce F2s through matings with F1s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F1 offspring can produce F2s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.
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Affiliation(s)
- Richard Allen
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Hannah Ryan
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Brian W. Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Charlotte King
- Department of Archaeology, Durham University, Science Site, Durham DH1 3LE, UK
- Department of Anatomy, University of Otago, Great King Street, Dunedin 9016, New Zealand
| | - Laurent Frantz
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Evan Irving-Pease
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Ross Barnett
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Anna Linderholm
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
- Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Liisa Loog
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - James Haile
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Mark White
- Department of Archaeology, Durham University, Science Site, Durham DH1 3LE, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 IJF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
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Admixture in Mammals and How to Understand Its Functional Implications. Bioessays 2019; 41:e1900123. [DOI: 10.1002/bies.201900123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Indexed: 12/13/2022]
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17
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Warren M. Suns, sloths and spy satellites - June's best science images. Nature 2019:10.1038/d41586-019-02074-w. [PMID: 32616885 DOI: 10.1038/d41586-019-02074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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