1
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Harding EF, Mercer LK, Yan GJH, Waters PD, White PA. Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes. Mol Biol Evol 2024; 41:msae160. [PMID: 39101626 PMCID: PMC11334065 DOI: 10.1093/molbev/msae160] [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: 11/30/2023] [Revised: 06/05/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Retroviruses are an ancient viral family that have globally coevolved with vertebrates and impacted their evolution. In Australia, a continent that has been geographically isolated for millions of years, little is known about retroviruses in wildlife, despite the devastating impacts of a retrovirus on endangered koala populations. We therefore sought to identify and characterize Australian retroviruses through reconstruction of endogenous retroviruses from marsupial genomes, in particular the Tasmanian devil due to its high cancer incidence. We screened 19 marsupial genomes and identified over 80,000 endogenous retrovirus fragments which we classified into eight retrovirus clades. The retroviruses were similar to either Betaretrovirus (5/8) or Gammaretrovirus (3/8) retroviruses, but formed distinct phylogenetic clades compared to extant retroviruses. One of the clades (MEBrv 3) lost an envelope but retained retrotranspositional activity, subsequently amplifying throughout all Dasyuridae genomes. Overall, we provide insights into Australian retrovirus evolution and identify a highly active endogenous retrovirus within Dasyuridae genomes.
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Affiliation(s)
- Emma F Harding
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Lewis K Mercer
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
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2
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Vincoff S, Schleupner B, Santos J, Morrison M, Zhang N, Dunphy-Daly MM, Eward WC, Armstrong AJ, Diana Z, Somarelli JA. The Known and Unknown: Investigating the Carcinogenic Potential of Plastic Additives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10445-10457. [PMID: 38830620 PMCID: PMC11191590 DOI: 10.1021/acs.est.3c06840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Abstract
Microplastics are routinely ingested and inhaled by humans and other organisms. Despite the frequency of plastic exposure, little is known about its health consequences. Of particular concern are plastic additives─chemical compounds that are intentionally or unintentionally added to plastics to improve functionality or as residual components of plastic production. Additives are often loosely bound to the plastic polymer and may be released during plastic exposures. To better understand the health effects of plastic additives, we performed a comprehensive literature search to compile a list of 2,712 known plastic additives. Then, we performed an integrated toxicogenomic analysis of these additives, utilizing cancer classifications and carcinogenic expression pathways as a primary focus. Screening these substances across two chemical databases revealed two key observations: (1) over 150 plastic additives have known carcinogenicity and (2) the majority (∼90%) of plastic additives lack data on carcinogenic end points. Analyses of additive usage patterns pinpointed specific polymers, functions, and products in which carcinogenic additives reside. Based on published chemical-gene interactions, both carcinogenic additives and additives with unknown carcinogenicity impacted similar biological pathways. The predominant pathways involved DNA damage, apoptosis, the immune response, viral diseases, and cancer. This study underscores the urgent need for a systematic and comprehensive carcinogenicity assessment of plastic additives and regulatory responses to mitigate the potential health risks of plastic exposure.
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Affiliation(s)
- Sophia Vincoff
- Department
of Medicine and the Duke Cancer Institute Center for Prostate and
Urologic Cancer, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Beatrice Schleupner
- Department
of Orthopaedics, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Jasmine Santos
- Department
of Medicine and the Duke Cancer Institute Center for Prostate and
Urologic Cancer, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Margaret Morrison
- Nicholas
School of the Environment, Duke University, Durham, North Carolina 27710, United States
| | - Newland Zhang
- Department
of Medicine and the Duke Cancer Institute Center for Prostate and
Urologic Cancer, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Meagan M. Dunphy-Daly
- Division
of Marine Science and Conservation, Nicholas School of the Environment,
Duke University Marine Laboratory, Duke
University, Beaufort, North Carolina 28516, United States
| | - William C. Eward
- Department
of Orthopaedics, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Andrew J. Armstrong
- Department
of Medicine and the Duke Cancer Institute Center for Prostate and
Urologic Cancer, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Zoie Diana
- Division
of Marine Science and Conservation, Nicholas School of the Environment,
Duke University Marine Laboratory, Duke
University, Beaufort, North Carolina 28516, United States
- Department
of Ecology and Evolutionary Biology, University
of Toronto, 25 Wilcocks
Street, Toronto, Ontario M5S3B2, Canada
| | - Jason A. Somarelli
- Department
of Medicine and the Duke Cancer Institute Center for Prostate and
Urologic Cancer, Duke University Medical
Center, Durham, North Carolina 27710, United States
- Nicholas
School of the Environment, Duke University, Durham, North Carolina 27710, United States
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3
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Bell O, Jones ME, Ruiz-Aravena M, Hamilton DG, Comte S, Hamer R, Hamede RK, Newton J, Bearhop S, McDonald RA. Human habitat modification, not apex scavenger decline, drives isotopic niche variation in a carnivore community. Oecologia 2024; 204:943-957. [PMID: 38619585 PMCID: PMC11062984 DOI: 10.1007/s00442-024-05544-9] [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: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 04/16/2024]
Abstract
Top carnivores can influence the structure of ecological communities, primarily through competition and predation; however, communities are also influenced by bottom-up forces such as anthropogenic habitat disturbance. Top carnivore declines will likely alter competitive dynamics within and amongst sympatric carnivore species. Increasing intraspecific competition is generally predicted to drive niche expansion and/or individual specialisation, while interspecific competition tends to constrain niches. Using stable isotope analysis of whiskers, we studied the effects of Tasmanian devil Sarcophilus harrisii declines upon the population- and individual-level isotopic niches of Tasmanian devils and sympatric spotted-tailed quolls Dasyurus maculatus subsp. maculatus. We investigated whether time since the onset of devil decline (a proxy for severity of decline) and landscape characteristics affected the isotopic niche breadth and overlap of devil and quoll populations. We quantified individual isotopic niche breadth for a subset of Tasmanian devils and spotted-tailed quolls and assessed whether between-site population niche variation was driven by individual-level specialisation. Tasmanian devils and spotted-tailed quolls demonstrated smaller population-level isotopic niche breadths with increasing human-modified habitat, while time since the onset of devil decline had no effect on population-level niche breadth or interspecific niche overlap. Individual isotopic niche breadths of Tasmanian devils and spotted-tailed quolls were narrower in human-modified landscapes, likely driving population isotopic niche contraction, however, the degree of individuals' specialisation relative to one another remained constant. Our results suggest that across varied landscapes, mammalian carnivore niches can be more sensitive to the bottom-up forces of anthropogenic habitat disturbance than to the top-down effects of top carnivore decline.
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Affiliation(s)
- Olivia Bell
- Environment and Sustainability Institute, University of Exeter, Penryn, TR10 9FE, UK
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia.
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, 14850, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
- Tasmanian Land Conservancy, 183 Macquarie Street, Hobart, TAS, 7007, Australia
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Road, Orange, NSW, 2800, Australia
| | - Rowena Hamer
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Jason Newton
- National Environmental Isotope Facility, Scottish Universities Environmental Research Centre, East Kilbride, G75 0QF, UK
| | - Stuart Bearhop
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, TR10 9FE, UK.
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4
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Stammnitz MR, Gori K, Murchison EP. No evidence that a transmissible cancer has shifted from emergence to endemism in Tasmanian devils. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231875. [PMID: 38633353 PMCID: PMC11022658 DOI: 10.1098/rsos.231875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
Tasmanian devils are endangered by a transmissible cancer known as Tasmanian devil facial tumour 1 (DFT1). A 2020 study by Patton et al. (Science 370, eabb9772 (doi:10.1126/science.abb9772)) used genome data from DFT1 tumours to produce a dated phylogenetic tree for this transmissible cancer lineage, and thence, using phylodynamics models, to estimate its epidemiological parameters and predict its future trajectory. It concluded that the effective reproduction number for DFT1 had declined to a value of one, and that the disease had shifted from emergence to endemism. We show that the study is based on erroneous mutation calls and flawed methodology, and that its conclusions cannot be substantiated.
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Affiliation(s)
- Maximilian R. Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Elizabeth P. Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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5
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Gallinson DG, Kozakiewicz CP, Rautsaw RM, Beer MA, Ruiz-Aravena M, Comte S, Hamilton DG, Kerlin DH, McCallum HI, Hamede R, Jones ME, Storfer A, McMinds R, Margres MJ. Intergenomic signatures of coevolution between Tasmanian devils and an infectious cancer. Proc Natl Acad Sci U S A 2024; 121:e2307780121. [PMID: 38466855 PMCID: PMC10962979 DOI: 10.1073/pnas.2307780121] [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: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
Coevolution is common and frequently governs host-pathogen interaction outcomes. Phenotypes underlying these interactions often manifest as the combined products of the genomes of interacting species, yet traditional quantitative trait mapping approaches ignore these intergenomic interactions. Devil facial tumor disease (DFTD), an infectious cancer afflicting Tasmanian devils (Sarcophilus harrisii), has decimated devil populations due to universal host susceptibility and a fatality rate approaching 100%. Here, we used a recently developed joint genome-wide association study (i.e., co-GWAS) approach, 15 y of mark-recapture data, and 960 genomes to identify intergenomic signatures of coevolution between devils and DFTD. Using a traditional GWA approach, we found that both devil and DFTD genomes explained a substantial proportion of variance in how quickly susceptible devils became infected, although genomic architectures differed across devils and DFTD; the devil genome had fewer loci of large effect whereas the DFTD genome had a more polygenic architecture. Using a co-GWA approach, devil-DFTD intergenomic interactions explained ~3× more variation in how quickly susceptible devils became infected than either genome alone, and the top genotype-by-genotype interactions were significantly enriched for cancer genes and signatures of selection. A devil regulatory mutation was associated with differential expression of a candidate cancer gene and showed putative allele matching effects with two DFTD coding sequence variants. Our results highlight the need to account for intergenomic interactions when investigating host-pathogen (co)evolution and emphasize the importance of such interactions when considering devil management strategies.
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Affiliation(s)
- Dylan G. Gallinson
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Christopher P. Kozakiewicz
- School of Biological Sciences, Washington State University, Pullman, WA99163
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI49060
| | - Rhett M. Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Marc A. Beer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY14853
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- New South Wales Department of Primary Industries, Vertebrate Pest Research Unit, Orange, NSW2800, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Douglas H. Kerlin
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Hamish I. McCallum
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD4111, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
- CANECEV Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier34394, France
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS7001, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA99163
| | - Ryan McMinds
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- College of Public Health, University of South Florida, Tampa, FL33620
| | - Mark J. Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
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6
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Raven N, Klaassen M, Madsen T, Jones M, Hamilton DG, Ruiz-Aravena M, Thomas F, Hamede RK, Ujvari B. Complex associations between cancer progression and immune gene expression reveals early influence of transmissible cancer on Tasmanian devils. Front Immunol 2024; 15:1286352. [PMID: 38515744 PMCID: PMC10954821 DOI: 10.3389/fimmu.2024.1286352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/29/2024] [Indexed: 03/23/2024] Open
Abstract
The world's largest extant carnivorous marsupial, the Tasmanian devil, is challenged by Devil Facial Tumor Disease (DFTD), a fatal, clonally transmitted cancer. In two decades, DFTD has spread across 95% of the species distributional range. A previous study has shown that factors such as season, geographic location, and infection with DFTD can impact the expression of immune genes in Tasmanian devils. To date, no study has investigated within-individual immune gene expression changes prior to and throughout the course of DFTD infection. To explore possible changes in immune response, we investigated four locations across Tasmania that differed in DFTD exposure history, ranging between 2 and >30 years. Our study demonstrated considerable complexity in the immune responses to DFTD. The same factors (sex, age, season, location and DFTD infection) affected immune gene expression both across and within devils, although seasonal and location specific variations were diminished in DFTD affected devils. We also found that expression of both adaptive and innate immune genes starts to alter early in DFTD infection and continues to change as DFTD progresses. A novel finding was that the lower expression of immune genes MHC-II, NKG2D and CD8 may predict susceptibility to earlier DFTD infection. A case study of a single devil with regressed tumor showed opposite/contrasting immune gene expression patterns compared to the general trends observed across devils with DFTD infection. Our study highlights the complexity of DFTD's interactions with the host immune system and the need for long-term studies to fully understand how DFTD alters the evolutionary trajectory of devil immunity.
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Affiliation(s)
- Nynke Raven
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Marcel Klaassen
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Thomas Madsen
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Manuel Ruiz-Aravena
- Mississippi State University, Forest & Wildlife Research Center (FWRC)-Wildlife, Fisheries & Aquaculture, Starkville, MS, United States
| | - Frederic Thomas
- CREEC/CANECEV, CREES-MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Beata Ujvari
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, VIC, Australia
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7
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Pollock TI, Hocking DP, Evans AR. Is a blunt sword pointless? Tooth wear impacts puncture performance in Tasmanian devil canines. J Exp Biol 2024; 227:jeb246925. [PMID: 38099427 PMCID: PMC10917061 DOI: 10.1242/jeb.246925] [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: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 02/01/2024]
Abstract
As teeth wear, their shapes change and functional features can be dulled or lost, presumably making them less effective for feeding. However, we do not know the magnitude and effect of this wear. Using Tasmanian devil canines as a case study, we investigated the impact of wear on puncture in pointed teeth. We measured aspects of shape impacted by wear (tip sharpness, height and volume) in teeth of varying wear followed by 3D printing of real and theoretical forms to carry out physical puncture tests. Tooth wear acts in two ways: by blunting tooth tips, and decreasing height and volume, both of which impact performance. Sharper tips in unworn teeth decrease the force and energy required to puncture compared with blunter worn teeth, while taller unworn teeth provide the continuous energy necessary to propagate fracture relative to shorter worn teeth. These wear-modulated changes in shape necessitate more than twice the force to drive worn teeth into ductile food and decrease the likelihood of puncture success.
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Affiliation(s)
- Tahlia I. Pollock
- The Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol BS8 1QU, UK
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - David P. Hocking
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Department of Zoology, Tasmanian Museum and Art Gallery, Hobart, TAS 7000, Australia
| | - Alistair R. Evans
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Museums Victoria Research Institute, Museums Victoria, Melbourne, VIC 3001, Australia
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8
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Olofsson P, Chipkin L, Daileda RC, Azevedo RBR. Mutational meltdown in asexual populations doomed to extinction. J Math Biol 2023; 87:88. [PMID: 37994999 DOI: 10.1007/s00285-023-02019-y] [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: 02/10/2023] [Revised: 07/03/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Asexual populations are expected to accumulate deleterious mutations through a process known as Muller's ratchet. Lynch and colleagues proposed that the ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze mutational meltdown using a multi-type branching process model where, in the presence of mutation, populations are doomed to extinction. We analyse the change in size and composition of the population and the time of extinction under this model.
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Affiliation(s)
- Peter Olofsson
- Department of Mathematics, Trinity University, San Antonio, TX, 78212, USA
- Department of Mathematics, Physics and Chemical Engineering, Jönköping University, 551 11, Jönköping, Sweden
| | - Logan Chipkin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ryan C Daileda
- Department of Mathematics, Trinity University, San Antonio, TX, 78212, USA
| | - Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.
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9
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Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evol 2023; 9:vead061. [PMID: 37941997 PMCID: PMC10630069 DOI: 10.1093/ve/vead061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
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Affiliation(s)
- Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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10
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Volery L, Vaz Fernandez M, Wegmann D, Bacher S. A general framework to quantify and compare ecological impacts under temporal dynamics. Ecol Lett 2023; 26:1726-1739. [PMID: 37515418 DOI: 10.1111/ele.14288] [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: 11/17/2022] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Biodiversity is diminishing at alarming rates due to multiple anthropogenic drivers. To mitigate these drivers, their impacts must be quantified accurately and comparably across drivers. To enable that, we present a generally applicable framework introducing fundamental principles of ecological impact quantification, including the quantification of interactions between multiple drivers. The framework contrasts biodiversity variables in impacted against those in unimpacted or other reference situations while accounting for their temporal dynamics through modelling. Properly accounting for temporal dynamics reduces biases in impact quantification and comparison. The framework addresses key questions around ecological impacts in global change science, namely, how to compare impacts under temporal dynamics across stressors, how to account for stressor interactions in such comparisons, and how to compare the success of management actions over time.
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Affiliation(s)
- Lara Volery
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Margarida Vaz Fernandez
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Sven Bacher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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11
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Burioli EAV, Hammel M, Vignal E, Vidal-Dupiol J, Mitta G, Thomas F, Bierne N, Destoumieux-Garzón D, Charrière GM. Transcriptomics of mussel transmissible cancer MtrBTN2 suggests accumulation of multiple cancer traits and oncogenic pathways shared among bilaterians. Open Biol 2023; 13:230259. [PMID: 37816387 PMCID: PMC10564563 DOI: 10.1098/rsob.230259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Transmissible cancer cell lines are rare biological entities giving rise to diseases at the crossroads of cancer and parasitic diseases. These malignant cells have acquired the amazing capacity to spread from host to host. They have been described only in dogs, Tasmanian devils and marine bivalves. The Mytilus trossulus bivalve transmissible neoplasia 2 (MtrBTN2) lineage has even acquired the capacity to spread inter-specifically between marine mussels of the Mytilus edulis complex worldwide. To identify the oncogenic processes underpinning the biology of these atypical cancers we performed transcriptomics of MtrBTN2 cells. Differential expression, enrichment, protein-protein interaction network, and targeted analyses were used. Overall, our results suggest the accumulation of multiple cancerous traits that may be linked to the long-term evolution of MtrBTN2. We also highlight that vertebrate and lophotrochozoan cancers could share a large panel of common drivers, which supports the hypothesis of an ancient origin of oncogenic processes in bilaterians.
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Affiliation(s)
- E A V Burioli
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - M Hammel
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - E Vignal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - J Vidal-Dupiol
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G Mitta
- IFREMER, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, Tahiti, Polynésie française
| | - F Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - N Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - D Destoumieux-Garzón
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G M Charrière
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
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12
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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13
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Stammnitz MR, Gori K, Kwon YM, Harry E, Martin FJ, Billis K, Cheng Y, Baez-Ortega A, Chow W, Comte S, Eggertsson H, Fox S, Hamede R, Jones M, Lazenby B, Peck S, Pye R, Quail MA, Swift K, Wang J, Wood J, Howe K, Stratton MR, Ning Z, Murchison EP. The evolution of two transmissible cancers in Tasmanian devils. Science 2023; 380:283-293. [PMID: 37079675 DOI: 10.1126/science.abq6453] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumor 1 (DFT1) and devil facial tumor 2 (DFT2). We investigated the genetic diversity and evolution of these clones by analyzing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled, chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982 to 1989) and DFT2 in 2011 (2009 to 2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions, and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA, but none are common to both cancers. This study reveals the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.
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Affiliation(s)
- Maximilian R Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Young Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Edward Harry
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Adrian Baez-Ortega
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange, NSW, Australia
| | | | - Samantha Fox
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
- Toledo Zoo, Toledo, OH, USA
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- CANCEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Billie Lazenby
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
| | - Sarah Peck
- Save the Tasmanian Devil Program, Tasmanian Department of Natural Resources and Environment, Hobart, TAS, Australia
| | - Ruth Pye
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Michael A Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kate Swift
- Mount Pleasant Laboratories, Tasmanian Department of Natural Resources and Environment, Prospect, TAS, Australia
| | - Jinhong Wang
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael R Stratton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zemin Ning
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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14
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Caley P, Barry SC. The effectiveness of citizen surveillance for detecting exotic vertebrates. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1012198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Citizen observations of the natural world are increasing in detail, growing in volume and increasingly being shared on web-based platforms for the purpose of sharing information and/or the crowd-sourcing of species identification. From a biosecurity perspective, such citizen data streams are important as they are responsible for the majority of post-border reports and most detections of exotic pest species of concern. The sharing of sightings amongst what are effectively communities of practice is a key driver of having the sighting of an exotic pest species recognized and reported. Whilst it is clear that the eyes, ears, cameras, and microphones of citizens are a major component of biosecurity surveillance, it is unclear what level of surveillance this provides in the prospective sense. As an example, what confidence does citizen science provide about “proof of absence” for exotic pests of concern? The taxonomy of surveillance used within the field of biosecurity would classify such citizen activities as contributing to “general surveillance,” for which non-detections are typically not recorded and methods of quantitative analysis are still under development. We argue that while not recorded, there is considerable information about citizens activities that routinely underpins peoples mental inference about the level of surveillance provided by citizen activities. Furthermore, we show that it is possible to make such inference from general surveillance transparent by describing and characterizing the activities that potentially generate sightings in a way that is amenable to quantitative analysis. In the context of evaluating surveillance provided by citizens for incursions of exotic vertebrates, we provide examples of citizen observations providing early warning and hence preventing the establishment of species from a range of animal groups. Historically, analysis of the power of general surveillance has been restricted to being conceptual, based on qualitative arguments. We provide this, but also provide a quantitative model framework and provide examples of how different forms of general surveillance data may be analyzed, particularly in supporting inference of eradication/extinction.
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15
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Pharmaceutics for free-ranging wildlife: Case studies to illustrate considerations and future prospects. Int J Pharm 2022; 628:122284. [DOI: 10.1016/j.ijpharm.2022.122284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022]
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16
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Kayigwe AN, M. Darby J, Lyons AB, L. Patchett A, Lisowski L, Liu GS, S. Flies A. A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The devil facial tumour disease (DFTD) has led to a massive decline in the wild Tasmanian devil (Sarcophilus harrisii) population. The disease is caused by two independent devil facial tumours (DFT1 and DFT2). These transmissible cancers have a mortality rate of nearly 100 %. An adenoviral vector-based vaccine has been proposed as a conservation strategy for the Tasmanian devil. This study aimed to determine if a human adenovirus serotype 5 could express functional transgenes in devil cells. As DFT1 cells do not constitutively express major histocompatibility complex class I (MHC-I), we developed a replication-deficient adenoviral vector that encodes devil interferon gamma (IFN-γ) fused to a fluorescent protein reporter. Our results show that adenoviral-expressed IFN-γ was able to stimulate upregulation of beta-2 microglobulin, a component of MHC-I, on DFT1, DFT2 and devil fibroblast cell lines. This work suggests that human adenoviruses can serve as a vaccine platform for devils and potentially other marsupials.
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Affiliation(s)
- Ahab N. Kayigwe
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Bibititi and Morogoro Rd Junction, P. O. Box 2958, Dar-es-salaam, Tanzania
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Jocelyn M. Darby
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - A. Bruce Lyons
- Tasmanian School of Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Amanda L. Patchett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Leszek Lisowski
- Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, 04-141 Warsaw, Poland
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, 3002, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
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17
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Fielding MW, Cunningham CX, Buettel JC, Stojanovic D, Yates LA, Jones ME, Brook BW. Dominant carnivore loss benefits native avian and invasive mammalian scavengers. Proc Biol Sci 2022; 289:20220521. [PMID: 36285494 PMCID: PMC9597402 DOI: 10.1098/rspb.2022.0521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Scavenging by large carnivores is integral for ecosystem functioning by limiting the build-up of carrion and facilitating widespread energy flows. However, top carnivores have declined across the world, triggering trophic shifts within ecosystems. Here, we compare findings from previous work on predator decline against areas with recent native mammalian carnivore loss. Specifically, we investigate top-down control on utilization of experimentally placed carcasses by two mesoscavengers—the invasive feral cat and native forest raven. Ravens profited most from carnivore loss, scavenging for five times longer in the absence of native mammalian carnivores. Cats scavenged on half of all carcasses in the region without dominant native carnivores. This was eight times more than in areas where other carnivores were at high densities. All carcasses persisted longer than the three-week monitoring period in the absence of native mammalian carnivores, while in areas with high carnivore abundance, all carcasses were fully consumed. Our results reveal that top-carnivore loss amplifies impacts associated with carnivore decline—increased carcass persistence and carrion access for smaller scavengers. This suggests that even at low densities, native mammalian carnivores can fulfil their ecological functions, demonstrating the significance of global carnivore conservation and supporting management approaches, such as trophic rewilding.
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Affiliation(s)
- Matthew W. Fielding
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Sandy Bay, Tasmania 7001, Australia
| | - Calum X. Cunningham
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Jessie C. Buettel
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Sandy Bay, Tasmania 7001, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | - Luke A. Yates
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Sandy Bay, Tasmania 7001, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
| | - Barry W. Brook
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Sandy Bay, Tasmania 7001, Australia
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18
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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19
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McLennan EA, Wise P, Lee AV, Grueber CE, Belov K, Hogg CJ. DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem. Ecol Evol 2022; 12:e8936. [PMID: 35600680 PMCID: PMC9120209 DOI: 10.1002/ece3.8936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species' native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species' native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short-tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.
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Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Phil Wise
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Andrew V. Lee
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Catherine E. Grueber
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Katherine Belov
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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20
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Hussey K, Caldwell A, Kreiss A, Skjødt K, Gastaldello A, Pye R, Hamede R, Woods GM, Siddle HV. Expression of the Nonclassical MHC Class I, Saha-UD in the Transmissible Cancer Devil Facial Tumour Disease (DFTD). Pathogens 2022; 11:pathogens11030351. [PMID: 35335675 PMCID: PMC8953681 DOI: 10.3390/pathogens11030351] [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: 01/31/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Devil facial tumour disease (DFTD) is a transmissible cancer that has circulated in the Tasmanian devil population for >25 years. Like other contagious cancers in dogs and devils, the way DFTD escapes the immune response of its host is a central question to understanding this disease. DFTD has a low major histocompatibility complex class I (MHC-I) expression due to epigenetic modifications, preventing host immune recognition of mismatched MHC-I molecules by T cells. However, the total MHC-I loss should result in natural killer (NK) cell activation due to the ‘missing self’. Here, we have investigated the expression of the nonclassical MHC-I, Saha-UD as a potential regulatory or suppressive mechanism for DFTD. A monoclonal antibody was generated against the devil Saha-UD that binds recombinant Saha-UD by Western blot, with limited crossreactivity to the classical MHC-I, Saha-UC and nonclassical Saha-UK. Using this antibody, we confirmed the expression of Saha-UD in 13 DFTD tumours by immunohistochemistry (n = 15) and demonstrated that Saha-UD expression is heterogeneous, with 12 tumours showing intratumour heterogeneity. Immunohistochemical staining for the Saha-UD showed distinct patterns of expression when compared with classical MHC-I molecules. The nonclassical Saha-UD expression by DFTD tumours in vivo may be a mechanism for immunosuppression, and further work is ongoing to characterise its ligand on immune cells.
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Affiliation(s)
- Kathryn Hussey
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (K.H.); (A.C.); (A.G.)
| | - Alison Caldwell
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (K.H.); (A.C.); (A.G.)
| | - Alexandre Kreiss
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia; (A.K.); (R.P.); (G.M.W.)
| | - Karsten Skjødt
- Department of Cancer and Inflammation, University of Southern Denmark, 5230 Odense, Denmark;
| | - Annalisa Gastaldello
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (K.H.); (A.C.); (A.G.)
| | - Ruth Pye
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia; (A.K.); (R.P.); (G.M.W.)
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7005, Australia;
| | - Gregory M. Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia; (A.K.); (R.P.); (G.M.W.)
| | - Hannah V. Siddle
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (K.H.); (A.C.); (A.G.)
- Correspondence:
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21
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URSID γ-HERPESVIRUS TYPE 1–RELATED VIRUS IN CAPTIVE BORNEAN SUN BEARS (HELARCTOS MALAYANUS EURYSPILUS) IN SABAH, MALAYSIA. J Zoo Wildl Med 2022; 53:92-99. [DOI: 10.1638/2021-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 11/21/2022] Open
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22
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Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022; 31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [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: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.
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Affiliation(s)
- N Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - M Klaassen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - T Madsen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - F Thomas
- CREEC/CANECEV (CREES), Montpellier, France.,MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - R Hamede
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia.,School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - B Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
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23
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Tissot S, Gérard AL, Boutry J, Dujon AM, Russel T, Siddle H, Tasiemski A, Meliani J, Hamede R, Roche B, Ujvari B, Thomas F. Transmissible Cancer Evolution: The Under-Estimated Role of Environmental Factors in the “Perfect Storm” Theory. Pathogens 2022; 11:pathogens11020241. [PMID: 35215185 PMCID: PMC8876101 DOI: 10.3390/pathogens11020241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022] Open
Abstract
Although the true prevalence of transmissible cancers is not known, these atypical malignancies are likely rare in the wild. The reasons behind this rarity are only partially understood, but the “Perfect Storm hypothesis” suggests that transmissible cancers are infrequent because a precise confluence of tumor and host traits is required for their emergence. This explanation is plausible as transmissible cancers, like all emerging pathogens, will need specific biotic and abiotic conditions to be able to not only emerge, but to spread to detectable levels. Because those conditions would be rarely met, transmissible cancers would rarely spread, and thus most of the time disappear, even though they would regularly appear. Thus, further research is needed to identify the most important factors that can facilitate or block the emergence of transmissible cancers and influence their evolution. Such investigations are particularly relevant given that human activities are increasingly encroaching into wild areas, altering ecosystems and their processes, which can influence the conditions needed for the emergence and spread of transmissible cell lines.
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Affiliation(s)
- Sophie Tissot
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Correspondence:
| | - Anne-Lise Gérard
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Justine Boutry
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
| | - Antoine M. Dujon
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Tracey Russel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia;
| | - Hannah Siddle
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK;
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Aurélie Tasiemski
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d’Infection et d’Immunité de Lille, 59000 Lille, France;
| | - Jordan Meliani
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Benjamin Roche
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinariay Zootecnia, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 01030, Mexico
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Frédéric Thomas
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
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24
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Grimaudo AT, Hoyt JR, Yamada SA, Herzog CJ, Bennett AB, Langwig KE. Host traits and environment interact to determine persistence of bat populations impacted by white-nose syndrome. Ecol Lett 2022; 25:483-497. [PMID: 34935272 PMCID: PMC9299823 DOI: 10.1111/ele.13942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022]
Abstract
Emerging infectious diseases have resulted in severe population declines across diverse taxa. In some instances, despite attributes associated with high extinction risk, disease emergence and host declines are followed by host stabilisation for unknown reasons. While host, pathogen, and the environment are recognised as important factors that interact to determine host-pathogen coexistence, they are often considered independently. Here, we use a translocation experiment to disentangle the role of host traits and environmental conditions in driving the persistence of remnant bat populations a decade after they declined 70-99% due to white-nose syndrome and subsequently stabilised. While survival was significantly higher than during the initial epidemic within all sites, protection from severe disease only existed within a narrow environmental space, suggesting host traits conducive to surviving disease are highly environmentally dependent. Ultimately, population persistence following pathogen invasion is the product of host-pathogen interactions that vary across a patchwork of environments.
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Affiliation(s)
| | - Joseph R. Hoyt
- Department of Biological SciencesVirginia TechBlacksburgVirginiaUSA
| | | | - Carl J. Herzog
- New York State Department of Environmental ConservationAlbanyNew YorkUSA
| | | | - Kate E. Langwig
- Department of Biological SciencesVirginia TechBlacksburgVirginiaUSA
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25
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Lewis AC, Hughes C, Rogers TL. Effects of intraspecific competition and body mass on diet specialization in a mammalian scavenger. Ecol Evol 2022; 12:e8338. [PMID: 35126999 PMCID: PMC8794717 DOI: 10.1002/ece3.8338] [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: 07/06/2021] [Revised: 09/26/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Animals that rely extensively on scavenging rather than hunting must exploit resources that are inherently patchy, dangerous, or subject to competition. Though it may be expected that scavengers should therefore form opportunistic feeding habits in order to survive, a broad species diet may mask specialization occurring at an individual level. To test this, we used stable isotope analysis to analyze the degree of specialization in the diet of the Tasmanian devil, one of few mammalian species to develop adaptations for scavenging. We found that the majority of individuals were dietary specialists, indicating that they fed within a narrow trophic niche despite their varied diet as a species. Even in competitive populations, only small individuals could be classified as true trophic generalists; larger animals in those populations were trophic specialists. In populations with reduced levels of competition, all individuals were capable of being trophic specialists. Heavier individuals showed a greater degree of trophic specialization, suggesting either that mass is an important driver of diet choice or that trophic specialization is an efficient foraging strategy allowing greater mass gain. Devils may be unique among scavenging mammals in the extent to which they can specialize their diets, having been released from the competitive pressure of larger carnivores.
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Affiliation(s)
- Anna C. Lewis
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
- The Carnivore ConservancyUlverstoneTasmaniaAustralia
| | - Channing Hughes
- The Carnivore ConservancyUlverstoneTasmaniaAustralia
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Tracey L. Rogers
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
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26
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Pollock TI, Hocking DP, Hunter DO, Parrott ML, Zabinskas M, Evans AR. Torn limb from limb: the ethology of prey-processing in Tasmanian devils (Sarcophilus harrisii). AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The success of carnivorous mammals is determined not only by their ability to locate and kill prey, but also their efficiency at consuming it. Breaking large prey into small pieces is challenging due to the strong and tough materials that make up a carcass (e.g. hide, muscle, and bone). Carnivores therefore require a diverse suite of prey-processing behaviours to utilise their catch. Tasmanian devils are Australia’s only large marsupial scavengers and have the ability to consume almost all of a carcass. To determine how they do this we analysed 5.5 hours of footage from 21 captive and wild devils feeding at carcasses. We documented 6320 bouts of 12 distinct prey-processing behaviours, performed at frequencies that varied throughout feeds and between groups. The time point in the feed influenced the types of behaviours used. This is likely due to changing prey size, as different techniques appear better suited to handling whole carcasses or large pieces (pulling and pinning) or smaller pieces (holding and manipulating). Group size impacted the frequency of social pulling behaviours, which increased with the number of animals. Our findings highlight the range of prey-processing behaviours performed by scavenging devils when handling, breaking down, and consuming a carcass. The devils’ repertoire shares similarities with large carnivores that handle and consume whole carcasses as well as small carnivores that are adept in grasping and handling smaller prey.
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27
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Penczykowski RM, Shocket MS, Ochs JH, Lemanski BCP, Sundar H, Duffy MA, Hall SR. Virulent Disease Epidemics Can Increase Host Density by Depressing Foraging of Hosts. Am Nat 2022; 199:75-90. [DOI: 10.1086/717175] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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28
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Durrant R, Hamede R, Wells K, Lurgi M. Disruption of Metapopulation Structure Reduces Tasmanian Devil Facial Tumour Disease Spread at the Expense of Abundance and Genetic Diversity. Pathogens 2021; 10:pathogens10121592. [PMID: 34959547 PMCID: PMC8705368 DOI: 10.3390/pathogens10121592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Metapopulation structure plays a fundamental role in the persistence of wildlife populations. It can also drive the spread of infectious diseases and transmissible cancers such as the Tasmanian devil facial tumour disease (DFTD). While disrupting this structure can reduce disease spread, it can also impair host resilience by disrupting gene flow and colonisation dynamics. Using an individual-based metapopulation model we investigated the synergistic effects of host dispersal, disease transmission rate and inter-individual contact distance for transmission, on the spread and persistence of DFTD from local to regional scales. Disease spread, and the ensuing population declines, are synergistically determined by individuals' dispersal, disease transmission rate and within-population mixing. Transmission rates can be magnified by high dispersal and inter-individual transmission distance. The isolation of local populations effectively reduced metapopulation-level disease prevalence but caused severe declines in metapopulation size and genetic diversity. The relative position of managed (i.e., isolated) local populations had a significant effect on disease prevalence, highlighting the importance of considering metapopulation structure when implementing metapopulation-scale disease control measures. Our findings suggest that population isolation is not an ideal management method for preventing disease spread in species inhabiting already fragmented landscapes, where genetic diversity and extinction risk are already a concern.
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Affiliation(s)
- Rowan Durrant
- Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, UK; (R.D.); (K.W.)
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Konstans Wells
- Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, UK; (R.D.); (K.W.)
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea SA2 8PP, UK; (R.D.); (K.W.)
- Correspondence: ; Tel.: +44-(0)-1792-602157
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29
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Owen RS, Ramarathinam SH, Bailey A, Gastaldello A, Hussey K, Skipp PJ, Purcell AW, Siddle HV. The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers. PLoS Pathog 2021; 17:e1010033. [PMID: 34780568 PMCID: PMC8629380 DOI: 10.1371/journal.ppat.1010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/29/2021] [Accepted: 10/13/2021] [Indexed: 01/04/2023] Open
Abstract
Contagious cancers are a rare pathogenic phenomenon in which cancer cells gain the ability to spread between genetically distinct hosts. Nine examples have been identified across marine bivalves, dogs and Tasmanian devils, but the Tasmanian devil is the only mammalian species known to have given rise to two distinct lineages of contagious cancer, termed Devil Facial Tumour 1 (DFT1) and 2 (DFT2). Remarkably, DFT1 and DFT2 arose independently from the same cell type, a Schwann cell, and while their ultra-structural features are highly similar they exhibit variation in their mutational signatures and infection dynamics. As such, DFT1 and DFT2 provide a unique framework for investigating how a common progenitor cell can give rise to distinct contagious cancers. Using a proteomics approach, we show that DFT1 and DFT2 are derived from Schwann cells in different differentiation states, with DFT2 carrying a molecular signature of a less well differentiated Schwann cell. Under inflammatory signals DFT1 and DFT2 have different gene expression profiles, most notably involving Schwann cell markers of differentiation, reflecting the influence of their distinct origins. Further, DFT2 cells express immune cell markers typically expressed during nerve repair, consistent with an ability to manipulate their extracellular environment, facilitating the cell’s ability to transmit between individuals. The emergence of two contagious cancers in the Tasmanian devil suggests that the inherent plasticity of Schwann cells confers a vulnerability to the formation of contagious cancers. Cancer can be an infectious pathogen, with nine known cases, infecting bivalves, dogs and two independent tumours circulating in the endangered Tasmanian devil. These cancers, known as Devil Facial Tumour 1 (DFT1) and Devil Facial Tumour 2 (DFT2), spread through the wild population much like parasites, moving between genetically distinct hosts during social biting behaviours and persisting in the population. As DFT1 and DFT2 are independent contagious cancers that arose from the same cell type, a Schwann cell, they provide a unique model system for studying the emergence of phenotypic variation in cancers derived from a single progenitor cell. In this study, we have shown that these two remarkably similar tumours have emerged from Schwann cells in different differentiation states. The differentiation state of the progenitor has altered the characteristics of each tumour, resulting in different responses to external signals. This work demonstrates that the cellular origin of infection can direct the phenotype of a contagious cancer and how it responds to signals from the host environment. Further, the plasticity of Schwann cells may make these cells more prone to forming contagious cancers, raising the possibility that further parasitic cancers could emerge from this cell type.
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Affiliation(s)
- Rachel S. Owen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Alistair Bailey
- Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Annalisa Gastaldello
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Kathryn Hussey
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Paul J. Skipp
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hannah V. Siddle
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- * E-mail:
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30
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Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves. Noncoding RNA 2021; 7:ncrna7040072. [PMID: 34842768 PMCID: PMC8628904 DOI: 10.3390/ncrna7040072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours.
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31
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Attard MRG, Lewis A, Wroe S, Hughes C, Rogers TL. Whisker growth in Tasmanian devils (
Sarcophilus harrisii
) and applications for stable isotope studies. Ecosphere 2021. [DOI: 10.1002/ecs2.3846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Marie R. G. Attard
- Department of Biological Sciences Royal Holloway University of London Egham TW20 0EX UK
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | - Anna Lewis
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
- The Carnivore Conservancy Ulverstone Tasmania Australia
| | - Stephen Wroe
- Function, Evolution and Anatomy Research Laboratory School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Channing Hughes
- The Carnivore Conservancy Ulverstone Tasmania Australia
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Tracey L. Rogers
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
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32
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Valenzuela-Sánchez A, Azat C, Cunningham AA, Delgado S, Bacigalupe LD, Beltrand J, Serrano JM, Sentenac H, Haddow N, Toledo V, Schmidt BR, Cayuela H. Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen. J Anim Ecol 2021; 91:308-319. [PMID: 34704260 DOI: 10.1111/1365-2656.13603] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/04/2021] [Indexed: 11/28/2022]
Abstract
Compensatory recruitment is a key demographic mechanism that has allowed the coexistence of populations of susceptible amphibians with Batrachochytrium dendrobatidis (Bd), a fungus causing one of the most devastating emerging infectious disease ever recorded among vertebrates. However, the underlying processes (e.g. density-dependent increase in survival at early life stages, change in reproductive traits) as well as the level of interpopulation variation in this response are poorly known. We explore potential mechanisms of compensatory recruitment in response to Bd infection by taking advantage of an amphibian system where male reproductive traits are easy to quantify in free-living populations. The Southern Darwin's frog Rhinoderma darwinii is a vocal sac-brooding species that exhibits a high susceptibility to lethal Bd infection. Using a 7-year capture-recapture study at four populations with contrasting Bd infection status (one high prevalence, one low prevalence and two Bd-free populations), we evaluated whether Bd-positive populations exhibited a higher adult recruitment and a higher male reproductive effort than Bd-negative populations. We also estimated population growth rates to explore whether recruitment compensated for the negative impacts of Bd on the survival of adults. In addition, we evaluated a potential demographic signal of compensatory recruitment (i.e. positive relationship between the proportion of juveniles and Bd prevalence) in response to Bd infection using raw count data from 13 R. darwinii populations. The high Bd prevalence population exhibited the highest male reproductive effort and the highest recruitment among the four monitored populations. This led to a growing population during the study period despite high mortality of adult hosts. In contrast, males from the population with low Bd prevalence had a low reproductive effort and this population, which had the lowest adult recruitment, was declining during the study period despite adults having a higher survival in comparison to the high Bd prevalence population. We also found a demographic signal of compensatory recruitment in response to Bd infection in our broader analysis of 13 R. darwinii populations. Our study underlines the importance of interpopulation variation in life-history strategies on the fate of host populations after infectious disease emergence. Our results also suggest that an increase in reproductive effort can be one of the processes underlying compensatory recruitment in populations of Bd-susceptible amphibians.
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Affiliation(s)
- Andrés Valenzuela-Sánchez
- ONG Ranita de Darwin, Valdivia, Chile.,Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile.,Sustainability Research Centre & PhD in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile
| | - Claudio Azat
- Sustainability Research Centre & PhD in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile
| | | | | | - Leonardo D Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - José M Serrano
- ONG Ranita de Darwin, Valdivia, Chile.,Museo de Zoología 'Alfonso L. Herrera', Departamento Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Sentenac
- Institute of Zoology, Zoological Society of London, London, UK.,Royal Veterinary College, University of London, London, UK
| | - Natashja Haddow
- Sustainability Research Centre & PhD in Conservation Medicine, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile.,Institute of Zoology, Zoological Society of London, London, UK.,Royal Veterinary College, University of London, London, UK
| | | | - Benedikt R Schmidt
- Info fauna karch, Neuchâtel, Switzerland.,Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Zürich, Switzerland
| | - Hugo Cayuela
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
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33
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Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection. BMC Genomics 2021; 22:698. [PMID: 34579650 PMCID: PMC8477496 DOI: 10.1186/s12864-021-07994-4] [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: 02/10/2021] [Accepted: 09/08/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown. RESULTS We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation. CONCLUSIONS Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.
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34
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Lazenby BT, Mooney NJ, Dickman CR. Raiders of the last ark: the impacts of feral cats on small mammals in Tasmanian forest ecosystems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02362. [PMID: 33899303 DOI: 10.1002/eap.2362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Feral individuals of the cat Felis catus are recognized internationally as a threat to biodiversity. Open, non-insular systems support a large proportion of the world's biodiversity, but the population-level impacts of feral cats in these systems are rarely elucidated. This limits prioritization and assessment of the effectiveness of management interventions. We quantified the predatory impact of feral cats on small mammals in open, non-insular forest systems in Tasmania, Australia in the context of other factors hypothesized to affect small mammal densities and survival, namely the density of a native carnivore, co-occurring small mammals, and rainfall. Change in feral cat density was the most important determinant of small mammal density and survival. We calculated that, on average, a 50% reduction in feral cat density could result in 25% and 10% increases in the density of the swamp rat Rattus lutreolus and long-tailed mouse Pseudomys higginsi, respectively. Low-level culling of feral cats that we conducted on two of our four study sites to experimentally alter feral cat densities revealed that swamp rat survival was highest when feral cat densities were stable. We conclude that feral cats exert downward pressure on populations of indigenous small mammals in temperate forest systems. However, alleviating this downward pressure on prey by culling a large proportion of the feral cat population is difficult as current methods for reducing feral cat populations in cool temperate forest systems are ineffective, and potentially even counterproductive. We suggest using an adaptive approach that regularly and robustly monitors how feral cats and small mammals respond to management interventions that are intended to conserve vulnerable prey species.
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Affiliation(s)
- B T Lazenby
- Department of Primary Industries, Parks, Water and Environment, 134 Macquarie Street, Hobart, Tasmania, Australia
| | - N J Mooney
- Tasmanian Museum and Art Gallery, Dunn Place, Hobart, Tasmania, Australia
| | - C R Dickman
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
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35
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Pollock TI, Parrott ML, Evans AR, Hocking DP. Wearing the devil down: Rate of tooth wear varies between wild and captive Tasmanian devils. Zoo Biol 2021; 40:444-457. [PMID: 34101216 DOI: 10.1002/zoo.21632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 01/28/2023]
Abstract
Mammalian carnivores rely on their sharp teeth to effectively kill and consume prey. However, over time this causes wear and breakage that alters tooth shape, reducing their effectiveness. Extreme tooth wear and damage is especially prevalent in species that scavenge carcasses, like the Tasmanian devil (Sarcophilus harrisii), which are well known for their voracious appetites and ability to consume almost all of a carcass, including bone. In this study, we comprehensively describe tooth wear in captive and wild devils to look for differences in the patterns and rate of wear between these environments. To do this we surveyed tooth condition in skulls from 182 wild and 114 captive devils for which age was estimated using canine over-eruption. We found the types of tooth wear documented were the same in captive and wild devils, but captive animals have less severe wear than wild devils of the same estimated age. There was no difference in the proportion of captive or wild individuals with broken canine or molar teeth; however, breakage occurred at a younger age in wild devils. Although not considered anomalous or harmful, this indicates a difference in the way teeth are being used and/or the foods consumed between captive and wild devils. We hypothesize how these results relate to differences in diet or behavior that may stem from their various feeding environments, for example, higher quality food (fresh, whole, and yet to be scavenged carcasses) provided to captive devils likely causes less wear. Further, we support management options that closely replicate wild diet items and behaviors suitable for a long-term insurance population.
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Affiliation(s)
- Tahlia I Pollock
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Marissa L Parrott
- Wildlife Conservation and Science, Zoos Victoria, Elliott Avenue, Parkville, Victoria, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Geosciences, Museums Victoria, Melbourne, Victoria, Australia
| | - David P Hocking
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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36
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Bell O, Jones ME, Cunningham CX, Ruiz‐Aravena M, Hamilton DG, Comte S, Hamede RK, Bearhop S, McDonald RA. Isotopic niche variation in Tasmanian devils Sarcophilus harrisii with progression of devil facial tumor disease. Ecol Evol 2021; 11:8038-8053. [PMID: 34188870 PMCID: PMC8216929 DOI: 10.1002/ece3.7636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Devil facial tumor disease (DFTD) is a transmissible cancer affecting Tasmanian devils Sarcophilus harrisii. The disease has caused severe population declines and is associated with demographic and behavioral changes, including earlier breeding, younger age structures, and reduced dispersal and social interactions. Devils are generally solitary, but social encounters are commonplace when feeding upon large carcasses. DFTD tumors can disfigure the jaw and mouth and so diseased individuals might alter their diets to enable ingestion of alternative foods, to avoid conspecific interactions, or to reduce competition. Using stable isotope analysis (δ13C and δ15N) of whiskers, we tested whether DFTD progression, measured as tumor volume, affected the isotope ratios and isotopic niches of 94 infected Tasmanian devils from six sites in Tasmania, comprising four eucalypt plantations, an area of smallholdings and a national park. Then, using tissue from 10 devils sampled before and after detection of tumors and 8 devils where no tumors were detected, we examined whether mean and standard deviation of δ13C and δ15N of the same individuals changed between healthy and diseased states. δ13C and δ15N values were generally not related to tumor volume in infected devils, though at one site, Freycinet National Park, δ15N values increased significantly as tumor volume increased. Infection with DFTD was not associated with significant changes in the mean or standard deviation of δ13C and δ15N values in individual devils sampled before and after detection of tumors. Our analysis suggests that devils tend to maintain their isotopic niche in the face of DFTD infection and progression, except where ecological conditions facilitate a shift in diets and feeding behaviors, demonstrating that ecological context, alongside disease severity, can modulate the behavioral responses of Tasmanian devils to DFTD.
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Affiliation(s)
- Olivia Bell
- Environment and Sustainability InstituteUniversity of ExeterPenrynUK
| | - Menna E. Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | | | - Manuel Ruiz‐Aravena
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - David G. Hamilton
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Sebastien Comte
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- Vertebrate Pest Research UnitNSW Department of Primary IndustriesOrangeNSWAustralia
| | - Rodrigo K. Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Stuart Bearhop
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
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37
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Genomics for conservation: a case study of behavioral genes in the Tasmanian devil. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Stahlke AR, Epstein B, Barbosa S, Margres MJ, Patton AH, Hendricks SA, Veillet A, Fraik AK, Schönfeld B, McCallum HI, Hamede R, Jones ME, Storfer A, Hohenlohe PA. Contemporary and historical selection in Tasmanian devils ( Sarcophilus harrisii) support novel, polygenic response to transmissible cancer. Proc Biol Sci 2021; 288:20210577. [PMID: 34034517 PMCID: PMC8150010 DOI: 10.1098/rspb.2021.0577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Tasmanian devils (Sarcophilus harrisii) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independently evolved transmissible cancer suggest that transmissible cancers may be a recurrent feature in devils. Here, we compared signatures of selection across temporal scales to determine whether genes or gene pathways under contemporary selection (six to eight generations) have also been subject to historical selection (65-85 Myr). First, we used targeted sequencing, RAD-capture, in approximately 2500 devils in six populations to identify genomic regions subject to rapid evolution. We documented genome-wide contemporary evolution, including 186 candidate genes related to cell cycling and immune response. Then we used a molecular evolution approach to identify historical positive selection in devils compared to other marsupials and found evidence of selection in 1773 genes. However, we found limited overlap across time scales, with only 16 shared candidate genes, and no overlap in enriched functional gene sets. Our results are consistent with a novel, multi-locus evolutionary response of devils to DFTD. Our results can inform conservation by identifying high priority targets for genetic monitoring and guiding maintenance of adaptive potential in managed populations.
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Affiliation(s)
- Amanda R. Stahlke
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Soraia Barbosa
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Sarah A. Hendricks
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Anne Veillet
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
| | - Alexandra K. Fraik
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Barbara Schönfeld
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Hamish I. McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844, USA
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39
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Cunningham CX, Comte S, McCallum H, Hamilton DG, Hamede R, Storfer A, Hollings T, Ruiz-Aravena M, Kerlin DH, Brook BW, Hocking G, Jones ME. Quantifying 25 years of disease-caused declines in Tasmanian devil populations: host density drives spatial pathogen spread. Ecol Lett 2021; 24:958-969. [PMID: 33638597 PMCID: PMC9844790 DOI: 10.1111/ele.13703] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/11/2020] [Accepted: 01/15/2021] [Indexed: 01/19/2023]
Abstract
Infectious diseases are strong drivers of wildlife population dynamics, however, empirical analyses from the early stages of pathogen emergence are rare. Tasmanian devil facial tumour disease (DFTD), discovered in 1996, provides the opportunity to study an epizootic from its inception. We use a pattern-oriented diffusion simulation to model the spatial spread of DFTD across the species' range and quantify population effects by jointly modelling multiple streams of data spanning 35 years. We estimate the wild devil population peaked at 53 000 in 1996, less than half of previous estimates. DFTD spread rapidly through high-density areas, with spread velocity slowing in areas of low host densities. By 2020, DFTD occupied >90% of the species' range, causing 82% declines in local densities and reducing the total population to 16 900. Encouragingly, our model forecasts the population decline should level-off within the next decade, supporting conservation management focused on facilitating evolution of resistance and tolerance.
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Affiliation(s)
- Calum X. Cunningham
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia,Correspondence: ;
| | - Sebastien Comte
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia,Vertebrate Pest Research Unit, NSW Department of Primary Industries, 1447 Forest Road, Orange, NSW 2800, Australia
| | - Hamish McCallum
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld 4111, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia,CANECEV – Centre de Recherches Ecologiques et Evolutives sur le cancer (CREEC), Montpellier 34090, France
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Tracey Hollings
- Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, Vic. 3084, Australia,School of BioSciences, The University of Melbourne, Parkville, Vic. 3010, Australia
| | - Manuel Ruiz-Aravena
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Douglas H. Kerlin
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld 4111, Australia
| | - Barry W. Brook
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia,ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Greg Hocking
- Game Services Tasmania, Tasmanian Department of Primary Industries, Parks, Water and Environment, TAS, PO Box 44, Hobart 7001, Australia
| | - Manna E. Jones
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
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40
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Ong CEB, Patchett AL, Darby JM, Chen J, Liu GS, Lyons AB, Woods GM, Flies AS. NLRC5 regulates expression of MHC-I and provides a target for anti-tumor immunity in transmissible cancers. J Cancer Res Clin Oncol 2021; 147:1973-1991. [PMID: 33797607 PMCID: PMC8017436 DOI: 10.1007/s00432-021-03601-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022]
Abstract
Purpose Downregulation of MHC class I (MHC-I) is a common immune evasion strategy of many cancers. Similarly, two allogeneic clonal transmissible cancers have killed thousands of wild Tasmanian devils (Sarcophilus harrisii) and also modulate MHC-I expression to evade anti-cancer and allograft responses. IFNG treatment restores MHC-I expression on devil facial tumor (DFT) cells but is insufficient to control tumor growth. Transcriptional co-activator NLRC5 is a master regulator of MHC-I in humans and mice but its role in transmissible cancers remains unknown. In this study, we explored the regulation and role of MHC-I in these unique genetically mis-matched tumors. Methods We used transcriptome and flow cytometric analyses to determine how MHC-I shapes allogeneic and anti-tumor responses. Cell lines that overexpress NLRC5 to drive antigen presentation, and B2M-knockout cell lines incapable of presenting antigen on MHC-I were used to probe the role of MHC-I in rare cases of tumor regressions. Results Transcriptomic results suggest that NLRC5 plays a major role in MHC-I regulation in devils. NLRC5 was shown to drive the expression of many components of the antigen presentation pathway but did not upregulate PDL1. Serum from devils with tumor regressions showed strong binding to IFNG-treated and NLRC5 cell lines; antibody binding to IFNG-treated and NRLC5 transgenic tumor cells was diminished or absent following B2M knockout. Conclusion MHC-I could be identified as a target for anti-tumor and allogeneic immunity. Consequently, NLRC5 could be a promising target for immunotherapy and vaccines to protect devils from transmissible cancers and inform development of transplant and cancer therapies for humans. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-021-03601-x.
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Affiliation(s)
- Chrissie E B Ong
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Amanda L Patchett
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Jocelyn M Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Jinying Chen
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.,Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Australia
| | - A Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Private Bag 23, Hobart TAS 7000, Australia.
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41
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Patchett AL, Tovar C, Blackburn NB, Woods GM, Lyons AB. Mesenchymal plasticity of devil facial tumour cells during in vivo vaccine and immunotherapy trials. Immunol Cell Biol 2021; 99:711-723. [PMID: 33667023 DOI: 10.1111/imcb.12451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/12/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Immune evasion is critical to the growth and survival of cancer cells. This is especially pertinent to transmissible cancers, which evade immune detection across genetically diverse hosts. The Tasmanian devil (Sarcophilus harrisii) is threatened by the emergence of Devil Facial Tumour Disease (DFTD), comprising two transmissible cancers (DFT1 and DFT2). The development of effective prophylactic vaccines and therapies against DFTD has been restricted by an incomplete understanding of how allogeneic DFT1 and DFT2 cells maintain immune evasion upon activation of tumour-specific immune responses. In this study, we used RNA sequencing to examine tumours from three experimental DFT1 cases. Two devils received a vaccine prior to inoculation with live DFT1 cells, providing an opportunity to explore changes to DFT1 cancers under immune pressure. Analysis of DFT1 in the non-immunised devil revealed a 'myelinating Schwann cell' phenotype, reflecting both natural DFT1 cancers and the DFT1 cell line used for the experimental challenge. Comparatively, immunised devils exhibited a 'dedifferentiated mesenchymal' DFT1 phenotype. A third 'immune-enriched' phenotype, characterised by increased PDL1 and CTLA-4 expression, was detected in a DFT1 tumour that arose after immunotherapy. In response to immune pressure, mesenchymal plasticity and upregulation of immune checkpoint molecules are used by human cancers to evade immune responses. Similar mechanisms are associated with immune evasion by DFTD cancers, providing novel insights that will inform modification of DFTD vaccines. As DFT1 and DFT2 are clonal cancers transmitted across genetically distinct hosts, the Tasmanian devil provides a 'natural' disease model for more broadly exploring these immune evasion mechanisms in cancer.
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Affiliation(s)
- Amanda L Patchett
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Cesar Tovar
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Nicholas B Blackburn
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - A Bruce Lyons
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
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42
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Carver S, Charleston M, Hocking G, Gales R, Driessen MM. Long‐Term Spatiotemporal Dynamics and Factors Associated with Trends in Bare‐Nosed Wombats. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Scott Carver
- Department of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania 7001 Australia
| | - Michael Charleston
- Department of Mathematics and Statistics University of Tasmania Tasmania Australia
| | - Gregory Hocking
- Department of Primary Industries, Parks, Water and Environment Tasmanian Government GPO Box 44 Hobart Tasmania 7000 Australia
| | - Rosemary Gales
- Department of Primary Industries, Parks, Water and Environment Tasmanian Government GPO Box 44 Hobart Tasmania 7000 Australia
| | - Michael M. Driessen
- Department of Primary Industries, Parks, Water and Environment Tasmanian Government GPO Box 44 Hobart Tasmania 7000 Australia
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43
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Reducing the Extinction Risk of Populations Threatened by Infectious Diseases. DIVERSITY 2021. [DOI: 10.3390/d13020063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential and become more susceptible to extinction due to other threats. Management of the genetic consequences of disease-induced population decline is often necessary. Whilst disease threats need to be addressed, they can be difficult to mitigate. Actions implemented to conserve the Tasmanian devil (Sarcophilus harrisii), which has suffered decline to the deadly devil facial tumour disease (DFTD), exemplify how genetic management can be used to reduce extinction risk in populations threatened by disease. Supplementation is an emerging conservation technique that may benefit populations threatened by disease by enabling gene flow and conserving their adaptive potential through genetic restoration. Other candidate species may benefit from genetic management via supplementation but concerns regarding outbreeding depression may prevent widespread incorporation of this technique into wildlife disease management. However, existing knowledge can be used to identify populations that would benefit from supplementation where risk of outbreeding depression is low. For populations threatened by disease and, in situations where disease eradication is not an option, wildlife managers should consider genetic management to buffer the host species against inbreeding and loss of genetic diversity.
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44
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Gastaldello A, Ramarathinam SH, Bailey A, Owen R, Turner S, Kontouli N, Elliott T, Skipp P, Purcell AW, Siddle HV. The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif. Immunology 2021; 163:169-184. [PMID: 33460454 PMCID: PMC8114214 DOI: 10.1111/imm.13307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 12/28/2022] Open
Abstract
Transmissible cancers are malignant cells that can spread between individuals of a population, akin to both a parasite and a mobile graft. The survival of the Tasmanian devil, the largest remaining marsupial carnivore, is threatened by the remarkable emergence of two independent lineages of transmissible cancer, devil facial tumour (DFT) 1 and devil facial tumour 2 (DFT2). To aid the development of a vaccine and to interrogate how histocompatibility barriers can be overcome, we analysed the peptides bound to major histocompatibility complex class I (MHC‐I) molecules from Tasmanian devil cells and representative cell lines of each transmissible cancer. Here, we show that DFT1 + IFN‐γ and DFT2 cell lines express a restricted repertoire of MHC‐I allotypes compared with fibroblast cells, potentially reducing the breadth of peptide presentation. Comparison of the peptidomes from DFT1 + IFNγ, DFT2 and host fibroblast cells demonstrates a dominant motif, despite differences in MHC‐I allotypes between the cell lines, with preference for a hydrophobic leucine residue at position 3 and position Ω of peptides. DFT1 and DFT2 both present peptides derived from neural proteins, which reflects a shared cellular origin that could be exploited for vaccine design. These results suggest that polymorphisms in MHC‐I molecules between tumours and host can be ‘hidden’ by a common peptide motif, providing the potential for permissive passage of infectious cells and demonstrating complexity in mammalian histocompatibility barriers.
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Affiliation(s)
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Alistair Bailey
- Centre for Cancer Immunology, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rachel Owen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Steven Turner
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - N Kontouli
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Tim Elliott
- Centre for Cancer Immunology, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Paul Skipp
- School of Biological Sciences, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and the Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hannah V Siddle
- School of Biological Sciences, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
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45
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Wong C, Darby JM, Murphy PR, Pinfold TL, Lennard PR, Woods GM, Lyons AB, Flies AS. Tasmanian devil CD28 and CTLA4 capture CD80 and CD86 from adjacent cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 115:103882. [PMID: 33039410 DOI: 10.1016/j.dci.2020.103882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Immune checkpoint immunotherapy is a pillar of human oncology treatment with potential for non-human species. The first checkpoint immunotherapy approved for human cancers targeted the CTLA4 protein. CTLA4 can inhibit T cell activation by capturing and internalizing CD80 and CD86 from antigen presenting cells, a process called trans-endocytosis. Similarly, CD28 can capture CD80 and CD86 via trogocytosis and retain the captured ligands on the surface of the CD28-expressing cells. The wild Tasmanian devil (Sarcophilus harrisii) population has declined by 77% due to transmissible cancers that evade immune defenses despite genetic mismatches between the host and tumors. We used a live cell-based assay to demonstrate that devil CTLA4 and CD28 can capture CD80 and CD86. Mutation of evolutionarily conserved motifs in CTLA4 altered functional interactions with CD80 and CD86 in accordance with patterns observed in other species. These results suggest that checkpoint immunotherapies can be translated to evolutionarily divergent species.
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Affiliation(s)
- Candida Wong
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Jocelyn M Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Peter R Murphy
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia; University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Terry L Pinfold
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Patrick R Lennard
- The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Gregory M Woods
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - A Bruce Lyons
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia.
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46
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Valenzuela-Sánchez A, Wilber MQ, Canessa S, Bacigalupe LD, Muths E, Schmidt BR, Cunningham AA, Ozgul A, Johnson PTJ, Cayuela H. Why disease ecology needs life-history theory: a host perspective. Ecol Lett 2021; 24:876-890. [PMID: 33492776 DOI: 10.1111/ele.13681] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022]
Abstract
When facing an emerging infectious disease of conservation concern, we often have little information on the nature of the host-parasite interaction to inform management decisions. However, it is becoming increasingly clear that the life-history strategies of host species can be predictive of individual- and population-level responses to infectious disease, even without detailed knowledge on the specifics of the host-parasite interaction. Here, we argue that a deeper integration of life-history theory into disease ecology is timely and necessary to improve our capacity to understand, predict and mitigate the impact of endemic and emerging infectious diseases in wild populations. Using wild vertebrates as an example, we show that host life-history characteristics influence host responses to parasitism at different levels of organisation, from individuals to communities. We also highlight knowledge gaps and future directions for the study of life-history and host responses to parasitism. We conclude by illustrating how this theoretical insight can inform the monitoring and control of infectious diseases in wildlife.
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Affiliation(s)
- Andrés Valenzuela-Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,ONG Ranita de Darwin, Valdivia and Santiago, Chile.,Centro de Investigación para la Sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Mark Q Wilber
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Wildlife Health, Department of Forestry, Wildlife and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Stefano Canessa
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Leonardo D Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Erin Muths
- U.S. Geological Survey, 2150 Centre Avenue Bldg C, Fort Collins, Colorado, 80526, USA
| | - Benedikt R Schmidt
- Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.,Info Fauna Karch, UniMail, Bâtiment G, Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Arpat Ozgul
- Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Pieter T J Johnson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Hugo Cayuela
- IBIS, Department of Biology, University Laval, Pavillon Charles-Eugène-Marchand, Avenue de la Médecine, Quebec City, Canada.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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47
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Pye R, Darby J, Flies AS, Fox S, Carver S, Elmer J, Swift K, Hogg C, Pemberton D, Woods G, Lyons AB. Post-release immune responses of Tasmanian devils vaccinated with an experimental devil facial tumour disease vaccine. WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr20210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
ContextDisease is increasingly becoming a driver of wildlife population declines and an extinction risk. Vaccines are one of the most successful health interventions in human history, but few have been tested for mitigating wildlife disease. The transmissible cancer, devil facial tumour disease (DFTD), triggered the Tasmanian devil’s (Sarcophilus harrisii) inclusion on the international endangered species list. In 2016, 33 devils from a DFTD-free insurance population were given an experimental DFTD vaccination before their wild release on the Tasmanian northern coast.
AimTo determine the efficacy of the vaccination protocol and the longevity of the induced responses.
MethodSix trapping trips took place over the 2.5 years following release, and both vaccinated and incumbent devils had blood samples and tumour biopsies collected.
Key resultsIn all, 8 of the 33 vaccinated devils were re-trapped, and six of those developed DFTD within the monitoring period. Despite the lack of protection provided by the vaccine, we observed signs of immune activation not usually found in unvaccinated devils. First, sera collected from the eight devils showed that anti-DFTD antibodies persisted for up to 2 years post-vaccination. Second, tumour-infiltrating lymphocytes were found in three of four biopsies collected from vaccinated devils, which contrasts with the ‘immune deserts’ typical of DFTs; only 1 of the 20 incumbent devils with DFTD had a tumour biopsy exhibiting immune-cell infiltrate. Third, immunohistochemical analysis of the vaccinated devils’ tumour biopsies identified the functional immune molecules associated with antigen-presenting cells (MHC-II) and T-cells (CD3), and the immune checkpoint molecule PD-1, all being associated with anti-tumour immunity in other species.
ConclusionsThese results correlate with our previous study on captive devils in which a prophylactic vaccine primed the devil immune system and, following DFTD challenge and tumour growth, immunotherapy induced complete tumour regressions. The field trial results presented here provide further evidence that the devil immune system can be primed to recognise DFTD cells, but additional immune manipulation could be needed for complete protection or induction of tumour regressions.
ImplicationsA protective DFTD vaccine would provide a valuable management approach for conservation of the Tasmanian devil.
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48
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Ohmer MEB, Costantini D, Czirják GÁ, Downs CJ, Ferguson LV, Flies A, Franklin CE, Kayigwe AN, Knutie S, Richards-Zawacki CL, Cramp RL. Applied ecoimmunology: using immunological tools to improve conservation efforts in a changing world. CONSERVATION PHYSIOLOGY 2021; 9:coab074. [PMID: 34512994 PMCID: PMC8422949 DOI: 10.1093/conphys/coab074] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 05/11/2023]
Abstract
Ecoimmunology is a rapidly developing field that explores how the environment shapes immune function, which in turn influences host-parasite relationships and disease outcomes. Host immune defence is a key fitness determinant because it underlies the capacity of animals to resist or tolerate potential infections. Importantly, immune function can be suppressed, depressed, reconfigured or stimulated by exposure to rapidly changing environmental drivers like temperature, pollutants and food availability. Thus, hosts may experience trade-offs resulting from altered investment in immune function under environmental stressors. As such, approaches in ecoimmunology can provide powerful tools to assist in the conservation of wildlife. Here, we provide case studies that explore the diverse ways that ecoimmunology can inform and advance conservation efforts, from understanding how Galapagos finches will fare with introduced parasites, to using methods from human oncology to design vaccines against a transmissible cancer in Tasmanian devils. In addition, we discuss the future of ecoimmunology and present 10 questions that can help guide this emerging field to better inform conservation decisions and biodiversity protection. From better linking changes in immune function to disease outcomes under different environmental conditions, to understanding how individual variation contributes to disease dynamics in wild populations, there is immense potential for ecoimmunology to inform the conservation of imperilled hosts in the face of new and re-emerging pathogens, in addition to improving the detection and management of emerging potential zoonoses.
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Affiliation(s)
- Michel E B Ohmer
- Living Earth Collaborative, Washington University in St. Louis, MO 63130, USA
| | - David Costantini
- Unité Physiologie Moléculaire et Adaptation (PhyMA), Muséum National d’Histoire Naturelle, CNRS, 57 Rue Cuvier, CP32, 75005, Paris, France
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
| | - Cynthia J Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Laura V Ferguson
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andy Flies
- Menzies Institute for Medical Research, University of Tasmania, Tasmania 7001, Australia
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, Queensland 4072, Australia
| | - Ahab N Kayigwe
- Menzies Institute for Medical Research, University of Tasmania, Tasmania 7001, Australia
| | - Sarah Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06268, USA
| | | | - Rebecca L Cramp
- School of Biological Sciences, The University of Queensland, Queensland 4072, Australia
- Corresponding author: School of Biological Sciences, The University of Queensland, Queensland 4072, Australia.
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49
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Patton AH, Lawrance MF, Margres MJ, Kozakiewicz CP, Hamede R, Ruiz-Aravena M, Hamilton DG, Comte S, Ricci LE, Taylor RL, Stadler T, Leaché A, McCallum H, Jones ME, Hohenlohe PA, Storfer A. A transmissible cancer shifts from emergence to endemism in Tasmanian devils. Science 2020; 370:370/6522/eabb9772. [PMID: 33303589 DOI: 10.1126/science.abb9772] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023]
Abstract
Emerging infectious diseases pose one of the greatest threats to human health and biodiversity. Phylodynamics is often used to infer epidemiological parameters essential for guiding intervention strategies for human viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Here, we applied phylodynamics to elucidate the epidemiological dynamics of Tasmanian devil facial tumor disease (DFTD), a fatal, transmissible cancer with a genome thousands of times larger than that of any virus. Despite prior predictions of devil extinction, transmission rates have declined precipitously from ~3.5 secondary infections per infected individual to ~1 at present. Thus, DFTD appears to be transitioning from emergence to endemism, lending hope for the continued survival of the endangered Tasmanian devil. More generally, our study demonstrates a new phylodynamic analytical framework that can be applied to virtually any pathogen.
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Affiliation(s)
- Austin H Patton
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.,Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Matthew F Lawrance
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | | | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia.,CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer (CREEC), Montpellier 34090, France
| | - Manuel Ruiz-Aravena
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - David G Hamilton
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Sebastien Comte
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia.,Vertebrate Pest Research Unit, Invasive Species and Biosecurity, NSW Department of Primary Industries, Orange, New South Wales 2800, Australia
| | - Lauren E Ricci
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.,Department of Wildland Resources, Utah State University, Logan, UT 84322, USA
| | - Robyn L Taylor
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Tanja Stadler
- Department for Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adam Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Hamish McCallum
- Vertebrate Pest Research Unit, Invasive Species and Biosecurity, NSW Department of Primary Industries, Orange, New South Wales 2800, Australia.,Environmental Futures Research Institute, Griffith University, Brisbane, Queensland 4111, Australia
| | - Menna E Jones
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Paul A Hohenlohe
- Department of Biological Science, University of Idaho, Moscow, ID 83844, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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50
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Hamilton DG, Jones ME, Cameron EZ, Kerlin DH, McCallum H, Storfer A, Hohenlohe PA, Hamede RK. Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils. Proc Biol Sci 2020; 287:20202454. [PMID: 33290679 PMCID: PMC7739934 DOI: 10.1098/rspb.2020.2454] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils (Sarcophilus harrisii) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark-recapture datasets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. The progression of DFTD negatively influences devils' likelihood of interaction within their network. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.
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Affiliation(s)
- David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Australia,e-mail:
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Elissa Z. Cameron
- School of Natural Sciences, University of Tasmania, Hobart, Australia,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Douglas H. Kerlin
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, USA
| | | | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia,CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer (CREEC), Montpellier 34090, France,e-mail:
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