• A demonstration of conservation genomics for threatened species management

      Wright, Belinda R.; Farquharson, Katherine A.; McLennan, Elspeth A.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2020)
      ... We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced‐representation sequencing (RRS) of 98 founders of the same programme. A subset of the WGS samples was also sequenced by RRS, allowing us to directly compare genome‐wide heterozygosity with estimates from RRS data. We found good congruence in interindividual variation and gene‐ontology classifications between the two data sets, indicating that our RRS data reflect the genome well....
    • Are any populations ‘safe’? Unexpected reproductive decline in a population of Tasmanian devils free of devil facial tumour disease

      Farquharson, Katherine A.; Gooley, Rebecca M.; Fox, S.; Huxtable, Stewart J.; Belov, Katherine; Pemberton, David; Hogg, Carolyn J.; Grueber, Catherine E. (2018)
      Conservation management relies on baseline demographic data of natural populations. For Tasmanian devils (Sarcophilus harrisii), threatened in the wild by two fatal and transmissible cancers (devil facial tumour disease DFTD: DFT1 and DFT2), understanding the characteristics of healthy populations is crucial for developing adaptive management strategies to bolster populations in the wild....
    • Assessing evolutionary processes over time in a conservation breeding program: A combined approach using molecular data, simulations and pedigree analysis

      Wright, Belinda R.; Hogg, Carolyn J.; McLennan, Elspeth A.; Belov, Katherine; Grueber, Catherine E. (2021)
      …We have quantified the effects of selection, drift and gene flow in 503 individuals across five generations from the Tasmanian devil insurance population. To determine whether different processes were acting in different settings, we separately analysed animals housed under individual-based management, versus those that were released to an island site. We found that a greater proportion of alleles were lost over time in the smaller island population than in captivity and propose that genetic drift is the most likely process influencing this result….
    • Characterization of reproductive gene diversity in the endangered Tasmanian devil

      Brandies, Parice A.; Wright, Belinda R.; Hogg, Carolyn J.; Grueber, Catherine E.; Belov, Katherine (2020)
      ...We characterized single nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in 37 Tasmanian devils…. We will use this information in future to examine the interplay between reproductive gene variation and reproductive fitness in Tasmanian devil populations.
    • Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian devils

      Patton, Austin H; Margres, Mark J; Stahlke, Amanda R; Hendricks, Sarah; Lewallen, Kevin; Hamede, Rodrigo K; Ruiz-Aravena, Manuel; Ryder, Oliver A.; McCallum, Hamish I; Jones, Menna E; et al. (2019)
      Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ?300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
    • Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs

      Farquharson, Katherine A.; Hogg, Carolyn J.; Belov, Katherine; Grueber, Catherine E. (2020)
      Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviors. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials; however, this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalized linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three nonmutually exclusive mate choice hypotheses: (a) advantage of heterozygous individuals, (b) advantage of dissimilar mates, and (c) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that nongenetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
    • Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population

      Wright, Belinda; Morris, Katrina; Grueber, Catherine E.; Willet, Cali E.; Gooley, Rebecca; Hogg, Carolyn J.; O’Meally, Denis; Hamede, Rodrigo; Jones, Menna; Wade, Claire; et al. (2015)
      The Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The tumor is one of only two naturally occurring transmissible cancers and is almost inevitably fatal. In 2006 a disease-free insurance population was established to ensure that the Tasmanian devil is protected from extinction. The insurance program is dependent upon preserving as much wild genetic diversity as possible to maximize the success of subsequent reintroductions to the wild. Accurate genotypic data is vital to the success of the program to ensure that loss of genetic diversity does not occur in captivity. Until recently, microsatellite markers have been used to study devil population genetics, however as genetic diversity is low in the devil and potentially decreasing in the captive population, a more sensitive genotyping assay is required.
    • Fecal viral diversity of captive and wild Tasmanian devils characterized using virion-enriched metagenomics and meta-transcriptomics

      Chong, Rowena; Shi, Mang; Grueber, Catherine E.; Holmes, Edward C.; Hogg, Carolyn J.; Belov, Katherine; Barrs, Vanessa R. (2019)
      The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils, and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and meta-transcriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from 2 captive and 4 wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses and a gammaherpesvirus were identified, as well as known mammalian pathogens such as rabbit haemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and meta-transcriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and meta-transcriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample. Importance: The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumour disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (DaHV-2), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and meta-transcriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.
    • From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

      Wright, Belinda R.; Farquharson, Katherine A.; McLennan, Elspeth A.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2019)
      Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes.
    • Genetic tools: maintaining genetic diversity in the Tasmanian devil metapopulation

      Grueber, Catherine E.; McLennan, Elspeth A.; Hogg, Carolyn J.; Fox, Samantha; Pemberton, David; Belov, Katherine (CSIROClayton South, Australia, 2019)
    • Genomic insights into a contagious cancer in Tasmanian devils

      Grueber, Catherine E.; Peel, Emma; Gooley, Rebecca; Belov, Katherine (2015)
      The Tasmanian devil faces extinction due to a contagious cancer…. From characterising immune genes and immune responses to studying tumour evolution, we have begun to uncover how a cancer can be ‘caught’ and are using genomic data to manage an insurance population of disease-free devils for the long-term survival of the species.
    • High blood lead concentrations in captive Tasmanian devils (Sarcophilus harrisii): a threat to the conservation of the species?

      Hivert, L. G.; Clarke, J. R.; Peck, S. J.; Lawrence, C.; Brown, W. E.; Huxtable, Stewart J.; Schaap, D.; Pemberton, David; Grueber, Catherine E. (2018)
      The Tasmanian devil (Sarcophilus harrisii) is the world’s largest extant marsupial carnivore. Since the emergence of devil facial tumour disease in 1996, the species has undergone a severe population decline....
    • Increasing generations in captivity is associated with increased vulnerability of Tasmanian devils to vehicle strike following release to the wild

      Grueber, Catherine E.; Reid-Wainscoat, Elizabeth E.; Fox, Samantha; Belov, Katherine; Shier, Debra M.; Hogg, Carolyn J.; Pemberton, David (2017)
      Captive breeding of threatened species, for release to the wild, is critical for conservation. This strategy, however, risks producing captive-raised animals with traits poorly suited to the wild. We describe the first study to characterise accumulated consequences of long-term captive breeding on behaviour, by following the release of Tasmanian devils to the wild. We test the impact of prolonged captive breeding on the probability that captive-raised animals are fatally struck by vehicles. Multiple generations of captive breeding increased the probability that individuals were fatally struck, a pattern that could not be explained by other confounding factors (e.g. age or release site). Our results imply that long-term captive breeding programs may produce animals that are naïve to the risks of the post-release environment. Our analyses have already induced changes in management policy of this endangered species, and serve as model of productive synergy between ecological monitoring and conservation strategy.
    • Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

      Morris, K.M.; Wright, B.; Grueber, Catherine E.; Hogg, Carolyn J.; Belov, Katherine (2015)
      The Tasmanian devil (S arcophilus harrisii ) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC ); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll‐like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNP s) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome‐level data from ten devils, SNP s within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole‐genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29–220 devils and found to contain 78 SNP s, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long‐term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad‐scale immunogenetic diversity analysis in threatened species.
    • Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore

      McLennan, E. A.; Grueber, Catherine E.; Wise, P.; Belov, K.; Hogg, Carolyn J. (2020)
      …We used an introduced population of Tasmanian devils Sarcophilus harrisii descended from two genetically differentiated source populations to illustrate the benefits of genetic admixture for translocation programmes. Devils are endangered due to an infectious cancer causing 80% population declines across their range since disease emergence in 1996…. As part of their conservation management, devils were introduced to Maria Island, Tasmania in an assisted colonization in 2012 with supplementations in 2013 and 2017….
    • No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding

      Gooley, Rebecca M.; Hogg, Carolyn J.; Belov, Katherine; Grueber, Catherine E. (2017)
      Inbreeding depression occurs when inbred individuals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 individuals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six diverse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in individual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.
    • Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species

      Farquharson, Katherine A.; Hogg, Carolyn J.; Grueber, Catherine E. (2017)
      Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals....
    • Pedigree reconstruction using molecular data reveals an early warning sign of gene diversity loss in an island population of Tasmanian devils (Sarcophilus harrisii)

      McLennan, Elspeth A.; Gooley, Rebecca M.; Wise, Phil; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2018)
      Tasmanian devils have experienced an 85% population decline since the emergence of an infectious cancer. In response, a captive insurance population was established in 2006 with a subpopulation later introduced onto Maria Island, Tasmania. We aimed to (1) examine the genetic parameters of the Maria Island population as a stand-alone site and within its broader metapopulation context, (2) assess the efficacy of assisted colonisations, and (3) inform future translocations. This study reconstructs the pedigree of 86 island-born devils using 31 polymorphic microsatellite loci. Combined molecular and pedigree analysis was used to monitor change in population genetic parameters in 4 years since colonisation. Molecular analysis alone revealed no significant change in genetic diversity, while DNA-reconstructed pedigree analysis revealed a statistically significant increase in inbreeding due to skewed founder representation. Pedigree modelling predicted that gene diversity would only be maintained above the threshold of 95% for a further 2 years, dropping to 77.1% after 40 years. Modelling alternative supplementation strategies revealed introducing eight new founders every 3 years will enable the population to retain 95% gene diversity until 2056, provided the translocated animals breed; to ensure this we recommend introducing ten new females every 3 years. We highlight the value of combining pedigree analyses with molecular data, from both a single-site and metapopulation viewpoint, for analysing changes in genetic parameters within populations of conservation concern. The importance of post-release genetic monitoring in an established population is emphasised, given how quickly inbreeding can accumulate and gene diversity be lost.
    • Reducing the extinction risk of populations threatened by infectious diseases

      Glassock, Gael L.; Grueber, Catherine E.; Belov, Katherine; Hogg, Carolyn J. (2021)
      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.
    • The effects of group versus intensive housing on the retention of genetic diversity in insurance populations

      Gooley, Rebecca M.; Hogg, Carolyn J.; Belov, Katherine; Grueber, Catherine E. (2018)
      Retention of genetic diversity and demographic sustainability are the cornerstones of conservation breeding success. In theory, monogamous breeding with equal reproductive output will retain genetic diversity in insurance populations more effectively than group housing which allows mate choice or intrasexual competition. However, the ecological relevance of group housing to a species can outweigh the theoretical benefits of forced monogamy. Here we investigated the influence of different types of captive housing (group (mate choice) versus intensive (forced monogamy)) on reproductive success, litter size and genetic diversity in the endangered Tasmanian devil (Sarcophilus harrisii).