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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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2
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Green C, Green DB, Ratcliffe N, Thompson D, Lea M, Baylis AMM, Bond AL, Bost C, Crofts S, Cuthbert RJ, González‐Solís J, Morrison KW, Poisbleau M, Pütz K, Rey AR, Ryan PG, Sagar PM, Steinfurth A, Thiebot J, Tierney M, Whitehead TO, Wotherspoon S, Hindell MA. Potential for redistribution of post-moult habitat for Eudyptes penguins in the Southern Ocean under future climate conditions. GLOBAL CHANGE BIOLOGY 2023; 29:648-667. [PMID: 36278894 PMCID: PMC10099906 DOI: 10.1111/gcb.16500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic climate change is resulting in spatial redistributions of many species. We assessed the potential effects of climate change on an abundant and widely distributed group of diving birds, Eudyptes penguins, which are the main avian consumers in the Southern Ocean in terms of biomass consumption. Despite their abundance, several of these species have undergone population declines over the past century, potentially due to changing oceanography and prey availability over the important winter months. We used light-based geolocation tracking data for 485 individuals deployed between 2006 and 2020 across 10 of the major breeding locations for five taxa of Eudyptes penguins. We used boosted regression tree modelling to quantify post-moult habitat preference for southern rockhopper (E. chrysocome), eastern rockhopper (E. filholi), northern rockhopper (E. moseleyi) and macaroni/royal (E. chrysolophus and E. schlegeli) penguins. We then modelled their redistribution under two climate change scenarios, representative concentration pathways RCP4.5 and RCP8.5 (for the end of the century, 2071-2100). As climate forcings differ regionally, we quantified redistribution in the Atlantic, Central Indian, East Indian, West Pacific and East Pacific regions. We found sea surface temperature and sea surface height to be the most important predictors of current habitat for these penguins; physical features that are changing rapidly in the Southern Ocean. Our results indicated that the less severe RCP4.5 would lead to less habitat loss than the more severe RCP8.5. The five taxa of penguin may experience a general poleward redistribution of their preferred habitat, but with contrasting effects in the (i) change in total area of preferred habitat under climate change (ii) according to geographic region and (iii) the species (macaroni/royal vs. rockhopper populations). Our results provide further understanding on the regional impacts and vulnerability of species to climate change.
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Affiliation(s)
- Cara‐Paige Green
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasmaniaAustralia
| | - David B. Green
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasmaniaAustralia
- ARC Australian Centre for Excellence in Antarctic ScienceInstitute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | | | - David Thompson
- National Institute of Water and Atmospheric Research Ltd.HataitaiWellingtonNew Zealand
| | - Mary‐Anne Lea
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasmaniaAustralia
- ARC Australian Centre for Excellence in Antarctic ScienceInstitute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Alastair M. M. Baylis
- South Atlantic Environmental Research InstituteStanleyFalkland Islands
- Macquarie UniversitySydneyNew South WalesAustralia
| | - Alexander L. Bond
- RSPB Centre for Conservation ScienceRoyal Society for the Protection of BirdsThe LodgeSandyUK
- Bird GroupNatural History MuseumTingUK
| | - Charles‐André Bost
- Centre d'Etudes Biologiques de ChizéUMR7372 CNRS‐La Rochelle UniversitéVilliers en BoisFrance
| | | | - Richard J. Cuthbert
- Royal Society for the Protection of BirdsCentre for Conservation ScienceCambridgeUK
- World Land TrustBlyth HouseHalesworthUK
| | - Jacob González‐Solís
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia EvolutivaEcologia i Ciències AmbientalsUniversitat de BarcelonaBarcelonaSpain
| | - Kyle W. Morrison
- National Institute of Water and Atmospheric Research Ltd.HataitaiWellingtonNew Zealand
| | - Maud Poisbleau
- Behavioural Ecology and Ecophysiology GroupDepartment of BiologyUniversity of AntwerpWilrijkBelgium
| | | | | | - Peter G. Ryan
- FitzPatrick Institute of African OrnithologyDST‐NRF Centre of ExcellenceUniversity of Cape TownRondeboschSouth Africa
| | - Paul M. Sagar
- National Institute of Water and Atmospheric Research Ltd.HataitaiWellingtonNew Zealand
| | - Antje Steinfurth
- Royal Society for the Protection of BirdsCentre for Conservation ScienceCambridgeUK
| | - Jean‐Baptiste Thiebot
- National Institute of Water and Atmospheric Research Ltd.ChristchurchNew Zealand
- Graduate School of Fisheries SciencesHokkaido UniversityHakodateJapan
| | - Megan Tierney
- South Atlantic Environmental Research InstituteStanleyFalkland Islands
- Joint Nature Conservation CommitteePeterboroughUK
| | - Thomas Otto Whitehead
- FitzPatrick Institute of African OrnithologyDST‐NRF Centre of ExcellenceUniversity of Cape TownRondeboschSouth Africa
| | - Simon Wotherspoon
- Australian Antarctic DivisionDepartment of Agriculture, Water and the EnvironmentAustralian Antarctic DivisionKingstonTasmaniaAustralia
| | - Mark A. Hindell
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasmaniaAustralia
- ARC Australian Centre for Excellence in Antarctic ScienceInstitute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
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3
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Shepherd LD, Miskelly CM, Bulgarella M, Tennyson AJD. Genomic analyses of fairy and fulmar prions (Procellariidae: Pachyptila spp.) reveals parallel evolution of bill morphology, and multiple species. PLoS One 2022; 17:e0275102. [PMID: 36166411 PMCID: PMC9514608 DOI: 10.1371/journal.pone.0275102] [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: 05/11/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Prions are small petrels that are abundant around the Southern Ocean. Here we use mitochondrial DNA (COI and cytochrome b) and nuclear reduced representation sequencing (ddRADseq) to examine the relationships within and between fairy (Pachyptila turtur) and fulmar (P. crassirostris) prions from across their distributions. We found that neither species was recovered as monophyletic, and that at least three species were represented. Furthermore, we detected several genetic lineages that are also morphologically distinct occurring in near sympatry at two locations (Snares Islands and Chatham Islands). The factors that have driven diversification in the fairy/fulmar prion complex are unclear but may include philopatry, differences in foraging distribution during breeding, differences in non-breeding distributions and breeding habitat characteristics. The observed distribution of genetic variation in the fairy/fulmar prion complex is consistent with population expansion from ice-free Last Glacial Maximum refugia into previously glaciated areas.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
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4
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Vaux F, Parvizi E, Craw D, Fraser CI, Waters J. Parallel recolonizations generate distinct genomic sectors in kelp following high-magnitude earthquake disturbance. Mol Ecol 2022; 31:4818-4831. [PMID: 35582778 PMCID: PMC9540901 DOI: 10.1111/mec.16535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post-earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial-genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.
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Affiliation(s)
- Felix Vaux
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Elahe Parvizi
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Dave Craw
- Department of GeologyUniversity of OtagoDunedinNew Zealand
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5
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Genomic insights into the secondary aquatic transition of penguins. Nat Commun 2022; 13:3912. [PMID: 35853876 PMCID: PMC9296559 DOI: 10.1038/s41467-022-31508-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth. This study examines the tempo and drivers of penguin diversification by combining genomes from all extant and recently extinct penguin lineages, stratigraphic data from fossil penguins and morphological and biogeographic data from all extant and extinct species. Together, these datasets provide new insights into the genetic basis and evolution of adaptations in penguins.
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6
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Miller AK, Timoshevskaya N, Smith JJ, Gillum J, Sharif S, Clarke S, Baker C, Kitson J, Gemmell NJ, Alexander A. Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). J Hered 2022; 113:380-397. [PMID: 35439308 PMCID: PMC9308044 DOI: 10.1093/jhered/esac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/23/2022] [Indexed: 11/12/2022] Open
Abstract
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.
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Affiliation(s)
- Allison K Miller
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Nataliya Timoshevskaya
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Joanne Gillum
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Saeed Sharif
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research Limited, PO Box 11 115, Hamilton 3251 New Zealand
| | - Jane Kitson
- Ngāi Tahu, Kitson Consulting Ltd, Invercargill/Waihopai, 9879, New Zealand
| | - Neil J Gemmell
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Alana Alexander
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
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7
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Fiddaman SR, Vinkler M, Spiro SG, Levy H, Emerling CA, Boyd AC, Dimopoulos EA, Vianna JA, Cole TL, Pan H, Fang M, Zhang G, Hart T, Frantz LAF, Smith AL. Adaptation and cryptic pseudogenization in penguin Toll-like Receptors. Mol Biol Evol 2021; 39:6460345. [PMID: 34897511 PMCID: PMC8788240 DOI: 10.1093/molbev/msab354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
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Affiliation(s)
- Steven R Fiddaman
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University Prague, Czech Republic
| | - Simon G Spiro
- Wildlife Health Services, Zoological Society of London Regent's Park, London, UK
| | - Hila Levy
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | | | - Amy C Boyd
- Jenner Institute, University of Oxford Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford Oxford, UK
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Theresa L Cole
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark
| | - Hailin Pan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Miaoquan Fang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Tom Hart
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Fogg Building, Queen Mary University of London Mile End Rd, Bethnal Green, London E1 4DQ, UK.,Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Germany
| | - Adrian L Smith
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
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8
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Shepherd LD, Miskelly CM, Cherel Y, Tennyson AJD. Genetic identification informs on the distributions of vagrant Royal (Eudyptes schlegeli) and Macaroni (Eudyptes chrysolophus) Penguins. Polar Biol 2021. [DOI: 10.1007/s00300-021-02961-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Parvizi E, Dutoit L, Fraser CI, Craw D, Waters JM. Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota. Mol Ecol 2021; 31:646-657. [PMID: 34695264 DOI: 10.1111/mec.16245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 01/05/2023]
Abstract
Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat-forming species can potentially influence the genetic diversity of large numbers of codistributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here, we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of cocolonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance-related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two codistributed species, one of which is an epibiotic amphipod and the other a subtidal macroalga, show few, if any, genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post-uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, codemographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events probably facilitated by macroalgal rafting. These results highlight that high-resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.
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Affiliation(s)
- Elahe Parvizi
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Dave Craw
- Department of Geology, University of Otago, Dunedin, New Zealand
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10
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Jenouvrier S, Che‐Castaldo J, Wolf S, Holland M, Labrousse S, LaRue M, Wienecke B, Fretwell P, Barbraud C, Greenwald N, Stroeve J, Trathan PN. The call of the emperor penguin: Legal responses to species threatened by climate change. GLOBAL CHANGE BIOLOGY 2021; 27:5008-5029. [PMID: 34342929 PMCID: PMC9291047 DOI: 10.1111/gcb.15806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 05/20/2023]
Abstract
Species extinction risk is accelerating due to anthropogenic climate change, making it urgent to protect vulnerable species through legal frameworks in order to facilitate conservation actions that help mitigate risk. Here, we discuss fundamental concepts for assessing climate change risks to species using the example of the emperor penguin (Aptenodytes forsteri), currently being considered for protection under the US Endangered Species Act (ESA). This species forms colonies on Antarctic sea ice, which is projected to significantly decline due to ongoing greenhouse gas (GHG) emissions. We project the dynamics of all known emperor penguin colonies under different GHG emission scenarios using a climate-dependent meta-population model including the effects of extreme climate events based on the observational satellite record of colonies. Assessments for listing species under the ESA require information about how species resiliency, redundancy and representation (3Rs) will be affected by threats within the foreseeable future. Our results show that if sea ice declines at the rate projected by climate models under current energy system trends and policies, the 3Rs would be dramatically reduced and almost all colonies would become quasi-extinct by 2100. We conclude that the species should be listed as threatened under the ESA.
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Affiliation(s)
- Stephanie Jenouvrier
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Judy Che‐Castaldo
- Conservation & Science DepartmentAlexander Center for Applied Population BiologyLincoln Park ZooChicagoIllinoisUSA
| | - Shaye Wolf
- Climate Law InstituteCenter for Biological DiversityOaklandCaliforniaUSA
| | - Marika Holland
- National Center for Atmospheric ResearchBoulderColoradoUSA
| | | | - Michelle LaRue
- School of Earth and EnvironmentUniversity of CanterburyChristchurchNew Zealand
- Department of Earth and Environmental SciencesUniversity of MinnesotaMinneapolisMinnesotaUSA
| | | | | | | | - Noah Greenwald
- Endangered Species ProgramCenter for Biological DiversityPortlandOregonUSA
| | - Julienne Stroeve
- Centre for Earth Observation ScienceUniversity of ManitobaWinnipegManitobaCanada
- National Snow and Ice Data CenterUSA Cooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderColoradoUSA
- Earth Sciences DepartmentUniversity College LondonLondonUK
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11
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Frugone MJ, Cole TL, López ME, Clucas G, Matos‐Maraví P, Lois NA, Pistorius P, Bonadonna F, Trathan P, Polanowski A, Wienecke B, Raya‐Rey A, Pütz K, Steinfurth A, Bi K, Wang‐Claypool CY, Waters JM, Bowie RCK, Poulin E, Vianna JA. Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- María José Frugone
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de Chile Valdivia Chile
| | - Theresa L. Cole
- Department of Zoology University of Otago Dunedin New Zealand
- Department of Biology, Ecology and Evolution University of Copenhagen Copenhagen Denmark
| | - María Eugenia López
- Department of Aquatic Resources Swedish University of Agricultural Sciences Drottningholm Sweden
| | - Gemma Clucas
- Atkinson Center for a Sustainable Future Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Cornell University Ithaca NY USA
| | - Pável Matos‐Maraví
- Biology Centre of the Czech Academy of SciencesInstitute of Entomology České Budějovice Czech Republic
| | - Nicolás A. Lois
- Departamento de Ecología Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Ecología Genética y Evolución de Buenos AiresConsejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires Argentina
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology Department of Zoology Nelson Mandela University Port Elizabeth South Africa
| | | | | | | | | | - Andrea Raya‐Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC‐CONICET) Ushuaia Argentina
- Wildlife Conservation Society Bronx NY USA
- Instituto de Ciencias Polares, Ambiente y Recursos NaturalesUniversidad Nacional de Tierra del Fuego Ushuaia Argentina
| | | | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology University of Cape Town Rondebosch South Africa
- RSPB Centre for Conservation Science Cambridge UK
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Cynthia Y. Wang‐Claypool
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | | | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Elie Poulin
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
| | - Juliana A. Vianna
- Pontificia Universidad Católica de ChileCenter for Genome RegulationFacultad de Agronomía e Ingeniería ForestalDepartamento de Ecosistemas y Medio Ambiente Santiago Chile
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12
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Effects of Diesel, Heavy Metals and Plastics Pollution on Penguins in Antarctica: A Review. Animals (Basel) 2021; 11:ani11092505. [PMID: 34573474 PMCID: PMC8465831 DOI: 10.3390/ani11092505] [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: 07/02/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Antarctica is contaminated by anthropogenic pollution. Due to the persistent low temperatures, the toxic impacts of pollution to the environment can be extensive. The severity of the effects varies according to the animal species, chemical type and level of exposure. Penguins are at major risk as they are the most prominent group of animals in Antarctica. This review highlights the background of penguins in Antarctica, the anthropogenic pollution and cases, as well as the toxic effects of diesel, heavy metals and microplastics toward penguins. A bibliometric analysis is also included. Abstract Antarctica is a relatively pristine continent that attracts scientists and tourists alike. However, the risk of environmental pollution in Antarctica is increasing with the increase in the number of visitors. Recently, there has been a surge in interest regarding diesel, heavy metals and microplastics pollution. Contamination from these pollutants poses risks to the environment and the health of organisms inhabiting the continent. Penguins are one of the most prominent and widely distributed animals in Antarctica and are at major risk due to pollution. Even on a small scale, the impacts of pollution toward penguin populations are extensive. This review discusses the background of penguins in Antarctica, the anthropogenic pollution and cases, as well as the impacts of diesel, heavy metals and microplastics toxicities on penguins. The trends of the literature for the emerging risks of these pollutants are also reviewed through a bibliometric approach and network mapping analysis. A sum of 27 articles are analyzed on the effects of varying pollutants on penguins in Antarctica from 2000 to 2020 using the VOSviewer bibliometric software, Microsoft Excel and Tableau Public. Research articles collected from the Scopus database are evaluated for the most applicable research themes according to the bibliometric indicators (articles, geography distribution, annual production, integrated subject areas, key source journals and keyword or term interactions). Although bibliometric studies on the present research theme are not frequent, our results are sub-optimal due to the small number of search query matches from the Scopus database. As a result, our findings offer only a fragmentary comprehension of the topics in question. Nevertheless, this review provides valuable inputs regarding prospective research avenues for researchers to pursue in the future.
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13
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Labrousse S, Fraser AD, Sumner M, Le Manach F, Sauser C, Horstmann I, Devane E, Delord K, Jenouvrier S, Barbraud C. Landfast ice: a major driver of reproductive success in a polar seabird. Biol Lett 2021; 17:20210097. [PMID: 34129795 PMCID: PMC8205520 DOI: 10.1098/rsbl.2021.0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/27/2021] [Indexed: 12/16/2022] Open
Abstract
In a fast-changing world, polar ecosystems are threatened by climate variability. Understanding the roles of fine-scale processes, and linear and nonlinear effects of climate factors on the demography of polar species is crucial for anticipating the future state of these fragile ecosystems. While the effects of sea ice on polar marine top predators are increasingly being studied, little is known about the impacts of landfast ice (LFI) on this species community. Based on a unique 39-year time series of satellite imagery and in situ meteorological conditions and on the world's longest dataset of emperor penguin (Aptenodytes forsteri) breeding parameters, we studied the effects of fine-scale variability of LFI and weather conditions on this species' reproductive success. We found that longer distances to the LFI edge (i.e. foraging areas) negatively affected the overall breeding success but also the fledging success. Climate window analyses suggested that chick mortality was particularly sensitive to LFI variability between August and November. Snowfall in May also affected hatching success. Given the sensitivity of LFI to storms and changes in wind direction, important future repercussions on the breeding habitat of emperor penguins are to be expected in the context of climate change.
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Affiliation(s)
- Sara Labrousse
- Sorbonne Universités, UPMC Université, Paris 06, UMR 7159, LOCEAN-IPSL, 75005 Paris, France
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Alexander D. Fraser
- Australian Antarctic Program Partnership, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Michael Sumner
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia
| | | | - Christophe Sauser
- Centre d’Études Biologiques de Chizé (CEBC), CNRS UMR 7372, 79360 Villiers en Bois, France
| | - Isabella Horstmann
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Eileen Devane
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Karine Delord
- Centre d’Études Biologiques de Chizé (CEBC), CNRS UMR 7372, 79360 Villiers en Bois, France
| | - Stéphanie Jenouvrier
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Christophe Barbraud
- Centre d’Études Biologiques de Chizé (CEBC), CNRS UMR 7372, 79360 Villiers en Bois, France
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14
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Westbury MV, Thompson KF, Louis M, Cabrera AA, Skovrind M, Castruita JAS, Constantine R, Stevens JR, Lorenzen ED. Ocean-wide genomic variation in Gray's beaked whales, Mesoplodon grayi. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201788. [PMID: 33959341 PMCID: PMC8074979 DOI: 10.1098/rsos.201788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale (Mesoplodon grayi) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa (n = 2) and South Australia (n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.
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Affiliation(s)
| | | | - M. Louis
- GLOBE Institute, University of Copenhagen, Denmark
| | | | - M. Skovrind
- GLOBE Institute, University of Copenhagen, Denmark
| | | | - R. Constantine
- School of Biological Sciences and Institute of Marine Science, University of Auckland, New Zealand
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15
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Bestley S, Ropert-Coudert Y, Bengtson Nash S, Brooks CM, Cotté C, Dewar M, Friedlaender AS, Jackson JA, Labrousse S, Lowther AD, McMahon CR, Phillips RA, Pistorius P, Puskic PS, Reis AODA, Reisinger RR, Santos M, Tarszisz E, Tixier P, Trathan PN, Wege M, Wienecke B. Marine Ecosystem Assessment for the Southern Ocean: Birds and Marine Mammals in a Changing Climate. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.566936] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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16
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Update on the global abundance and distribution of breeding Gentoo Penguins (Pygoscelis papua). Polar Biol 2020. [DOI: 10.1007/s00300-020-02759-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Groff DV, Hamley KM, Lessard TJR, Greenawalt KE, Yasuhara M, Brickle P, Gill JL. Seabird establishment during regional cooling drove a terrestrial ecosystem shift 5000 years ago. SCIENCE ADVANCES 2020; 6:6/43/eabb2788. [PMID: 33097535 PMCID: PMC7608832 DOI: 10.1126/sciadv.abb2788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
The coastal tussac (Poa flabellata) grasslands of the Falkland Islands are a critical seabird breeding habitat but have been drastically reduced by grazing and erosion. Meanwhile, the sensitivity of seabirds and tussac to climate change is unknown because of a lack of long-term records in the South Atlantic. Our 14,000-year multiproxy record reveals an ecosystem state shift following seabird establishment 5000 years ago, as marine-derived nutrients from guano facilitated tussac establishment, peat productivity, and increased fire. Seabird arrival coincided with regional cooling, suggesting that the Falkland Islands are a cold-climate refugium. Conservation efforts focusing on tussac restoration should include this terrestrial-marine linkage, although a warming Southern Ocean calls into question the long-term viability of the Falkland Islands as habitat for low-latitude seabirds.
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Affiliation(s)
- Dulcinea V Groff
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming 82071, USA.
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Climate Change Institute, University of Maine, Orono, ME 04469, USA
| | - Kit M Hamley
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Climate Change Institute, University of Maine, Orono, ME 04469, USA
| | - Trevor J R Lessard
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Climate Change Institute, University of Maine, Orono, ME 04469, USA
| | | | - Moriaki Yasuhara
- School of Biological Sciences and Swire Institute of Marine Science, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Paul Brickle
- South Atlantic Environmental Research Institute, Ross Road, Stanley FIQQ 1ZZ, Falkland Islands
- School of Biological Sciences (Zoology), University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, Scotland, UK
| | - Jacquelyn L Gill
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA.
- Climate Change Institute, University of Maine, Orono, ME 04469, USA
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18
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Hillis D, McKechnie I, Guiry E, St Claire DE, Darimont CT. Ancient dog diets on the Pacific Northwest Coast: zooarchaeological and stable isotope modelling evidence from Tseshaht territory and beyond. Sci Rep 2020; 10:15630. [PMID: 33004834 PMCID: PMC7530995 DOI: 10.1038/s41598-020-71574-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/18/2020] [Indexed: 10/29/2022] Open
Abstract
Domestic dogs are frequently encountered in Indigenous archaeological sites on the Northwest Coast of North America. Although dogs depended on human communities for care and provisioning, archaeologists lack information about the specific foods dogs consumed. Previous research has used stable isotope analysis of dog diets for insight into human subsistence ('canine surrogacy' model) and identified considerable use of marine resources. Here, we use zooarchaeological data to develop and apply a Bayesian mixing model (MixSIAR) to estimate dietary composition from 14 domestic dogs and 13 potential prey taxa from four archaeological sites (2,900-300 BP) in Tseshaht First Nation territory on western Vancouver Island, British Columbia, Canada. Two candidate models that best match zooarchaeological data indicate dogs predominantly consumed salmon and forage fish (35-65%), followed by nearshore fish (4-40%), and marine mammals (2-30%). We compared these isotopic data to dogs across the Northwest Coast, which indicated a pronounced marine diet for Tseshaht dogs and, presumably, their human providers. These results are broadly consistent with the canine surrogacy model as well as help illuminate human participation in pre-industrial marine food webs and the long-term role of fisheries in Indigenous economies and lifeways.
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Affiliation(s)
- Dylan Hillis
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8P 5C2, Canada.,Department of Geography, University of Victoria, Victoria, BC, Canada
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8P 5C2, Canada. .,Hakai Institute, Heriot Bay, Quadra Island, BC, Canada.
| | - Eric Guiry
- Department of Anthropology, Trent University, Peterborough, ON, Canada.,School of Archaeology and Ancient History, University of Leicester, Leicester, UK.,Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
| | - Denis E St Claire
- Tseshaht First Nation, Port Alberni, BC, Canada.,Coast Heritage Consulting, Victoria, BC, Canada
| | - Chris T Darimont
- Department of Geography, University of Victoria, Victoria, BC, Canada.,Hakai Institute, Heriot Bay, Quadra Island, BC, Canada.,Raincoast Conservation Foundation, Sidney, BC, Canada
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19
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Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula. Viruses 2020; 12:v12091029. [PMID: 32947826 PMCID: PMC7551938 DOI: 10.3390/v12091029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.
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20
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Abstract
Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (N e ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased N e between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.
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21
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Louis M, Skovrind M, Samaniego Castruita JA, Garilao C, Kaschner K, Gopalakrishnan S, Haile JS, Lydersen C, Kovacs KM, Garde E, Heide-Jørgensen MP, Postma L, Ferguson SH, Willerslev E, Lorenzen ED. Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros. Proc Biol Sci 2020; 287:20192964. [PMID: 32315590 PMCID: PMC7211449 DOI: 10.1098/rspb.2019.2964] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (Monodon monoceros) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyse 121 complete mitochondrial genomes from narwhals sampled across their range and use them in combination with species distribution models to elucidate the influence of past and ongoing climatic shifts on their population structure and demographic history. We find low levels of genetic diversity and limited geographic structuring of genetic clades. We show that narwhals experienced a long-term low effective population size, which increased after the Last Glacial Maximum, when the amount of suitable habitat expanded. Similar post-glacial habitat release has been a key driver of population size expansion of other polar marine predators. Our analyses indicate that habitat availability has been critical to the success of narwhals, raising concerns for their fate in an increasingly warming Arctic.
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Affiliation(s)
- Marie Louis
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mikkel Skovrind
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Cristina Garilao
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, 79106 Freiburg, Germany
| | - Shyam Gopalakrishnan
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - James S. Haile
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Kit M. Kovacs
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Eva Garde
- Greenland Institute of Natural Resources, Strandgade 91,2, DK-1401 CopenhagenDenmark
| | | | - Lianne Postma
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada
| | - Steven H. Ferguson
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada
| | - Eske Willerslev
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- D-IAS, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Eline D. Lorenzen
- Globe Institute, Universityof Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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22
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Abstract
Climate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postglacial reductions in sea ice drove biological shifts across multiple widespread Southern Ocean species. We test for demographic shifts driven by climate events over recent millennia by analyzing population genomic datasets spanning 3 penguin genera (Eudyptes, Pygoscelis, and Aptenodytes). Demographic analyses for multiple species (macaroni/royal, eastern rockhopper, Adélie, gentoo, king, and emperor) currently inhabiting southern coastlines affected by heavy sea ice conditions during the Last Glacial Maximum (LGM) yielded genetic signatures of near-simultaneous population expansions associated with postglacial warming. Populations of the ice-adapted emperor penguin are inferred to have expanded slightly earlier than those of species requiring ice-free terrain. These concerted high-latitude expansion events contrast with relatively stable or declining demographic histories inferred for 4 penguin species (northern rockhopper, western rockhopper, Fiordland crested, and Snares crested) that apparently persisted throughout the LGM in ice-free habitats. Limited genetic structure detected in all ice-affected species across the vast Southern Ocean may reflect both rapid postglacial colonization of subantarctic and Antarctic shores, in addition to recent genetic exchange among populations. Together, these analyses highlight dramatic, ecosystem-wide responses to past Southern Ocean climate change and suggest potential for further shifts as warming continues.
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