1
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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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2
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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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3
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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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4
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [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: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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5
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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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6
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Fuochi S, Galligioni V. Disease Animal Models for Cancer Research. Methods Mol Biol 2023; 2645:105-125. [PMID: 37202613 DOI: 10.1007/978-1-0716-3056-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite nonanimal methods (NAMs) are more and more exploited and new NAMs are developed and validated, animal models are still used in cancer research. Animals are used at multiple levels, from understanding molecular traits and pathways, to mimicking clinical aspects of tumor progression, to drug testing. In vivo approaches are not trivial and involve cross-disciplinary knowledge: animal biology and physiology, genetics, pathology, and animal welfare.The aim of this chapter is not to list and address all animal models used in cancer research. Instead, the authors would like to guide experimenters in the strategies to adopt in both planning and performing in vivo experimental procedures, including the choice of cancer animal models.
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Affiliation(s)
- Sara Fuochi
- Universität Bern, Experimental Animal Center, Bern, Switzerland
| | - Viola Galligioni
- Netherlands Institute for Neuroscience - KNAW, Amsterdam, The Netherlands.
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7
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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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8
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Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox ( Urocyon littoralis catalinae). Genes (Basel) 2022; 13:1496. [PMID: 36011407 PMCID: PMC9408614 DOI: 10.3390/genes13081496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 12/12/2022] Open
Abstract
Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007-2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population.
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Affiliation(s)
- Sarah A. Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Julie L. King
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Calvin L. Duncan
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Winston Vickers
- Institute for Wildlife Studies, Arcata, CA 95521, USA
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
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9
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Dujon AM, Boutry J, Tissot S, Lemaître JF, Boddy AM, Gérard AL, Alvergne A, Arnal A, Vincze O, Nicolas D, Giraudeau M, Telonis-Scott M, Schultz A, Pujol P, Biro PA, Beckmann C, Hamede R, Roche B, Ujvari B, Thomas F. Cancer Susceptibility as a Cost of Reproduction and Contributor to Life History Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.861103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reproduction is one of the most energetically demanding life-history stages. As a result, breeding individuals often experience trade-offs, where energy is diverted away from maintenance (cell repair, immune function) toward reproduction. While it is increasingly acknowledged that oncogenic processes are omnipresent, evolving and opportunistic entities in the bodies of metazoans, the associations among reproductive activities, energy expenditure, and the dynamics of malignant cells have rarely been studied. Here, we review the diverse ways in which age-specific reproductive performance (e.g., reproductive aging patterns) and cancer risks throughout the life course may be linked via trade-offs or other mechanisms, as well as discuss situations where trade-offs may not exist. We argue that the interactions between host–oncogenic processes should play a significant role in life-history theory, and suggest some avenues for future research.
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10
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Functional diversity in the RAS subfamily of small GTPases. Biochem Soc Trans 2022; 50:921-933. [PMID: 35356965 DOI: 10.1042/bst20211166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
RAS small GTPases regulate important signalling pathways and are notorious drivers of cancer development and progression. While most research to date has focused on understanding and addressing the oncogenic potential of three RAS oncogenes: HRAS, KRAS, and NRAS; the full RAS subfamily is composed of 35 related GTPases with diverse cellular functions. Most remain deeply understudied despite strong evolutionary conservation. Here, we highlight a group of 17 poorly characterized RAS GTPases that are frequently down-regulated in cancer and evidence suggests may function not as oncogenes, but as tumour suppressors. These GTPases remain largely enigmatic in terms of their cellular function, regulation, and interaction with effector proteins. They cluster within two families we designate as 'distal-RAS' (D-RAS; comprised of DIRAS, RASD, and RASL10) and 'CaaX-Less RAS' (CL-RAS; comprised of RGK, NKIRAS, RERG, and RASL11/12 GTPases). Evidence of a tumour suppressive role for many of these GTPases supports the premise that RAS subfamily proteins may collectively regulate cellular proliferation.
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11
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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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12
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Drawert B, Flies AS, Matthew S, Powell M, Rumsey B. Saving the Devils Is in the Details: Tasmanian Devil Facial Tumor Disease Can Be Eliminated with Interventions. LETTERS IN BIOMATHEMATICS 2022; 9:121-140. [PMID: 37655234 PMCID: PMC10470821 DOI: 10.30707/lib9.1.1681913305.269822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Tasmanian Devils facial tumor disease (DFTD) is severely impacting the population of this wild animal. We developed a computational model of the population of Tasmanian Devils, and the change induced by DFTD. We use this model to test possible intervention strategies Tasmanian conservationists could do. We investigate bait drop vaccination programs, diseased animal removals programs, and evolution of natural immunity. We conclude that a combination of intervention strategies gives the most favorable outcome. An additional goal of this paper is reproducibility of our results. Our StochSS software platform features the ability to share and reproduce the computational notebooks that created all of the results in the paper. We endeavor that all readers should be able to reproduce our results with minimum effort.
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Affiliation(s)
- Brian Drawert
- National Environmental Modeling and Analysis Center, University of North Carolina Asheville, Asheville, NC, USA
| | - Andrew S. Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Sean Matthew
- National Environmental Modeling and Analysis Center, University of North Carolina Asheville, Asheville, NC, USA
| | - Megan Powell
- Department of Mathematics and Statistics, University of North Carolina Asheville, Asheville, NC, USA
| | - Bryan Rumsey
- National Environmental Modeling and Analysis Center, University of North Carolina Asheville, Asheville, NC, USA
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13
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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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14
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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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15
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Stenvinkel P, Avesani CM, Gordon LJ, Schalling M, Shiels PG. Biomimetics provides lessons from nature for contemporary ways to improve human health. J Clin Transl Sci 2021; 5:e128. [PMID: 34367673 PMCID: PMC8327543 DOI: 10.1017/cts.2021.790] [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: 04/09/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Homo sapiens is currently living in serious disharmony with the rest of the natural world. For our species to survive, and for our well-being, we must gather knowledge from multiple perspectives and actively engage in studies of planetary health. The enormous diversity of species, one of the most striking aspects of life on our planet, provides a source of solutions that have been developed through evolution by natural selection by animals living in extreme environments. The food system is central to finding solutions; our current global eating patterns have a negative impact on human health, driven climate change and loss of biodiversity. We propose that the use of solutions derived from nature, an approach termed biomimetics, could mitigate the effects of a changing climate on planetary health as well as human health. For example, activation of the transcription factor Nrf2 may play a role in protecting animals living in extreme environments, or animals exposed to heat stress, pollution and pesticides. In order to meet these challenges, we call for the creation of novel interdisciplinary planetary health research teams.
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Affiliation(s)
- Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, Stockholm, Sweden
| | - Carla M. Avesani
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, Stockholm, Sweden
| | - Line J. Gordon
- Stockholm Resilience Centre Stockholm University, Stockholm, Sweden
| | - Martin Schalling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paul G. Shiels
- Institute of Cancer Sciences, Wolfson Wohl Translational Research Centre, University of Glasgow, Bearsden, Glasgow, UK
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16
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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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17
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Hamede R, Madsen T, McCallum H, Storfer A, Hohenlohe PA, Siddle H, Kaufman J, Giraudeau M, Jones M, Thomas F, Ujvari B. Darwin, the devil, and the management of transmissible cancers. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:748-751. [PMID: 32992406 PMCID: PMC8048418 DOI: 10.1111/cobi.13644] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/01/2020] [Accepted: 08/14/2020] [Indexed: 05/05/2023]
Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Thomas Madsen
- School of Biological SciencesUniversity of WollongongWollongongNew South WalesAustralia
| | - Hamish McCallum
- School of Environment and ScienceGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWAU.S.A.
| | - Paul A. Hohenlohe
- Department of Biological SciencesInstitute for Bioinformatics and Evolutionary Studies, University of IdahoMoscowIDU.S.A.
| | - Hannah Siddle
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonSO17 1BJU.K.
| | - Jim Kaufman
- Department of PathologyUniversity of CambridgeCambridgeCB2 1QPU.K.
| | - Mathieu Giraudeau
- Centre de Recherches Ecologiques et Evolutives sur le Cancer/Centre National de la Recherche ScientifiqueMontpellierFrance
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Frédéric Thomas
- Centre de Recherches Ecologiques et Evolutives sur le Cancer/Centre National de la Recherche ScientifiqueMontpellierFrance
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
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18
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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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19
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Kozakiewicz CP, Ricci L, Patton AH, Stahlke AR, Hendricks SA, Margres MJ, Ruiz-Aravena M, Hamilton DG, Hamede R, McCallum H, Jones ME, Hohenlohe PA, Storfer A. Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour. Mol Ecol 2020; 29:3217-3233. [PMID: 32682353 PMCID: PMC9805799 DOI: 10.1111/mec.15558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission.
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Affiliation(s)
| | - Lauren Ricci
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Austin H. Patton
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Amanda R. Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Sarah A. Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Mark J. Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Ruiz-Aravena
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - David G. Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA,corresponding author: Andrew Storfer, School of Biological Sciences, Washington State University, Pullman, WA, USA.
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