Genomic insights into a contagious cancer in Tasmanian devils

Grueber, Catherine E.; Peel, Emma; Gooley, Rebecca M.; Belov, Katherine

doi:10.1016/j.tig.2015.05.001

Cited by 24 publications

(15 citation statements)

References 73 publications

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“…This pattern has been explained by the fixation of the same alleles across multiple MHC loci (drift across loci; Eimes et al 2011), or by the effects of PMBS itself when PMBS distorts allele frequency and the alleles are fixed/lost with higher frequency than alleles in neutral loci (Ejsmond & Radwan 2011). Drift was shown to be a predominant force in several studies that investigated the dynamics between genetic drift and PMBS in populations that experienced a recent bottleneck event (Miller & Lambert 2004b;Eimes et al 2011;Strand et al 2012;Grueber et al 2013Grueber et al , 2015Sutton et al 2015;Gonzalez-Quevedo et al 2015). On the other hand, several studies have shown that PMBS may counteract the effect of random genetic drift and maintain MHC diversity in spite of small population size (Aguilar et al 2004;Van Oosterhout et al 2006) or a recent bottleneck (Oliver & Piertney 2012).…”

Section: Introductionmentioning

confidence: 99%

Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds

et al. 2016

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The extracellular subunit of the major histocompatibility complex MHCIIβ plays an important role in the recognition of pathogens and the initiation of the adaptive immune response of vertebrates. It is widely accepted that pathogen-mediated selection in combination with neutral micro-evolutionary forces (e.g. genetic drift) shape the diversity of MHCIIβ, but it has proved difficult to determine the relative effects of these forces. We evaluated the effect of genetic drift and balancing selection on MHCIIβ diversity in 12 small populations of Galápagos mockingbirds belonging to four different species, and one larger population of the Northern mockingbird from the continental USA. After genotyping MHCIIβ loci by high-throughput sequencing, we applied a correlational approach to explore the relationships between MHCIIβ diversity and population size by proxy of island size. As expected when drift predominates, we found a positive effect of population size on the number of MHCIIβ alleles present in a population. However, the number of MHCIIβ alleles per individual and number of supertypes were not correlated with population size. This discrepancy points to an interesting feature of MHCIIβ diversity dynamics: some levels of diversity might be shaped by genetic drift while others are independent and possibly maintained by balancing selection.

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Section: Introductionmentioning

confidence: 99%

Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds

et al. 2016

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“…Devil facial tumour disease (DFTD) is an emergent transmissible lethal cancer exclusive to Tasmanian devils (Sarcophilus harrisii) and is threatening the species with extinction in the wild (Pye et al, 2016). Recently, genomic approaches have been brought to bear on DFTD (Deakin & Belov, 2012;Grueber et al, 2015;Pye et al, 2016). Devil facial tumour disease results in an extremely high rate of adult fatalities, with some wild populations already having been reduced by 95% (Deakin & Belov, 2012).…”

Section: Wildlife Disease Case Study 4: Tasmanian Devil Facial Tumourmentioning

confidence: 99%

Precision wildlife medicine: applications of the human‐centred precision medicine revolution to species conservation

Whilde

Martindale

Duffy

2016

Global Change Biology

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The current species extinction crisis is being exacerbated by an increased rate of emergence of epizootic disease. Human-induced factors including habitat degradation, loss of biodiversity and wildlife population reductions resulting in reduced genetic variation are accelerating disease emergence. Novel, efficient and effective approaches are required to combat these epizootic events. Here, we present the case for the application of human precision medicine approaches to wildlife medicine in order to enhance species conservation efforts. We consider how the precision medicine revolution, coupled with the advances made in genomics, may provide a powerful and feasible approach to identifying and treating wildlife diseases in a targeted, effective and streamlined manner. A number of case studies of threatened species are presented which demonstrate the applicability of precision medicine to wildlife conservation, including sea turtles, amphibians and Tasmanian devils. These examples show how species conservation could be improved by using precision medicine techniques to determine novel treatments and management strategies for the specific medical conditions hampering efforts to restore population levels. Additionally, a precision medicine approach to wildlife health has in turn the potential to provide deeper insights into human health and the possibility of stemming and alleviating the impacts of zoonotic diseases. The integration of the currently emerging Precision Medicine Initiative with the concepts of EcoHealth (aiming for sustainable health of people, animals and ecosystems through transdisciplinary action research) and One Health (recognizing the intimate connection of humans, animal and ecosystem health and addressing a wide range of risks at the animal-human-ecosystem interface through a coordinated, collaborative, interdisciplinary approach) has great potential to deliver a deeper and broader interdisciplinary-based understanding of both wildlife and human diseases.

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“…The DFTD cancer threatens the survival of the species and was one of the reasons to sequence the Tasmanian devil genome. 17,[21][22] The first Australian marsupial to have its genome sequenced was that of the tammar wallaby, but the assembly is currently highly fragmented 15 and has not allowed detailed TE analyses. Thus, the genome data of the Tasmanian devil offer a chance to analyze the TE composition and dynamics in an Australian marsupial genome and compare it to other mammalian species.…”

Section: Transposable Elements and Evolutionmentioning

confidence: 99%

The devil is in the details: Transposable element analysis of the Tasmanian devil genome

Nilsson

2015

Mobile Genetic Elements

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The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome.

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Genomic insights into a contagious cancer in Tasmanian devils

Cited by 24 publications

References 73 publications

Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds

Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds

Precision wildlife medicine: applications of the human‐centred precision medicine revolution to species conservation

The devil is in the details: Transposable element analysis of the Tasmanian devil genome

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