Tag Archives: Luke Silver

Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot

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Type: Journal article

Reference: Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol. 2025 Mar 25:e17746. doi: 10.1111/mec.17746.

Abstract

Loss of genetic diversity threatens a species’ adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.

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Academic Adventures to the Other Side of the Globe

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by Luke Silver (Post-doc)

In August of 2024 I had the exciting opportunity to undertake a three-month research stay in the Institute of Evolutionary Ecology and Conservation Genomics at Ulm University. So how did this come about?

Professor Simone Sommer was one of my thesis reviewers and she reached out to Kathy and Carolyn with an opportunity to combine my skillset in genomes and MHC annotation with some newly generated bat sequences. So at the start of August, I departed Sydney for an almost 30 hour journey to the city of Ulm (about 1 hour west of Munich) in southern Germany. Upon arrival at Ulm train station, I was met by a postdoc Dr Dominik Melville who showed me to my accommodation for the next three months. With no German language knowledge, I headed to the supermarket and managed to annoy the person at the register by not pre-weighing my fruits and vegetables – just one of many times that having some German language skills would have come in handy.

The purpose of my visit was to manually annotate genes of a crucial immune gene family known as the major histocompatibility complex (MHC) in bats. These genes form molecules with are expressed on cell surfaces and are responsible for detecting self and non -self and presenting foreign pathogen derived peptides to other cells of the immune system. We were able to leverage the recently released data from phase 1 of the Bat1K project (a consortium that aims to sequence the genomes of all living bat species around the world).

I also managed to find time to sample plenty of the local delicacies of beer and pretzels  and to travel in the local area including to the beautiful Lake Konstanz, Stuttgart, Nuremberg, Vienna, Salzburg and Prague. This is just a small example of how science can lead to new and exciting experiences and opportunities.

Luke Silver

Dr Luke Silver’s research is focused on generating and using genomic and transcriptomic resources for threatened Australian species. He used these resources to investigate the evolution of the immune system and study how diversity within immune genes is linked to disease traits. He has experience in characterisation of complex immune gene families, in particular the major histocompatibility complex which is a key component of the adaptive immune system

@LukeSilver20

AMPed Up Immunity: 418 Whole Genomes Reveal Intraspecific Diversity of Koala Antimicrobial Peptides

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Type: Journal article

Reference: Petrohilos C, Peel E, Silver LW, Belov K, Hogg CJ. AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides. Immunogenetics. 2025 Jan 8;77(1):11. doi: 10.1007/s00251-024-01368-2.

Abstract

Characterising functional diversity is a vital element to understanding a species’ immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species’ range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.

A reference genome for the eastern bettong ( Bettongia gaimardi)

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Type: Journal article

Reference: Silver, L. W., Edwards, R. J., Neaves, L., Manning, A. D., Hogg, C. J., & Banks, S. (2025). A reference genome for the eastern bettong ( Bettongia gaimardi). F1000Research, 13, 1544. https://doi.org/10.12688/f1000research.157851.1

Abstract

The eastern or Tasmanian bettong ( Bettongia gaimardi) is one of four extant bettong species and is listed as ‘Near Threatened’ by the IUCN. We sequenced short read data on the 10x system to generate a reference genome 3.46Gb in size and contig N50 of 87.36Kb and scaffold N50 of 2.93Mb. Additionally, we used GeMoMa to provide and accompanying annotation for the reference genome. The generation of a reference genome for the eastern bettong provides a vital resource for the conservation of the species.

Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution

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Type: Journal article

Reference: Cui J, Batley KC, Silver LW, McLennan EA, Hogg CJ, Belov K. Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution. Immunogenetics. 2024 Nov 30;77(1):5. doi: 10.1007/s00251-024-01365-5

Abstract

The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species’ range, however, is not even. Toll-like receptors (TLRs) play a crucial role in innate immunity by recognising and responding to various pathogens. Variations in TLR genes can influence an individual’s susceptibility or resistance to infectious diseases. The aim of this study was to identify koala TLR diversity across the east coast of Australia using 413 re-sequenced genomes at 30 × coverage. We identified 45 single-nucleotide polymorphisms (SNP) leading to 51 alleles within ten TLR genes. Our results show that the diversity of TLR genes in the koala forms four distinct genetic groups, which are consistent with the diversity of the koala major histocompatibility complex (MHC), another key immune gene family. The bioinformatics approach presented here has broad applicability to other threatened species with existing genomic resources.

Genomics identifies koala populations at risk across eastern Australia

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Type: Journal article

Reference: McLennan, Elspeth A., Toby G. L. Kovacs, Luke W. Silver, Zhiliang Chen, Frederick R. Jaya, Simon Y. W. Ho, Katherine Belov, and Carolyn J. Hogg. 2025. “ Genomics Identifies Koala Populations at Risk across Eastern Australia.” Ecological Applications 35(1): e3062. https://doi.org/10.1002/eap.3062

Abstract

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega-fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future-proofed baseline genomic dataset across the koala’s range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid-coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.

Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

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Type: Journal article

Reference: Silver LW, McLennan EA, Beaman J, da Silva KB, Timms P, Hogg CJ, Belov K. Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas. Immunogenetics. 2024 Dec;76(5-6):381-395. doi: 10.1007/s00251-024-01356-6

Abstract

Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

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Type: Journal article

Reference: Hogg, C.J., Edwards, R.J., Farquharson, K.A. et al. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8, 1311–1326 (2024). https://doi.org/10.1038/s41559-024-02436-2

Abstract

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

The future is here: an easy-to-use toolkit for integrating genetics into conservation management

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Type: Journal article

Reference: Hogg, C.J., Farquharson, K.A., Brandies, P., Silver, L.W., Ottewell, K., McLennan, E.A., Richmond, S. and Belov, K. (2025), The future is here: an easy-to-use toolkit for integrating genetics into conservation management. Anim Conserv, 28: 93-103. https://doi.org/10.1111/acv.12971

Abstract

Over the past decade, the development of genetic and genomic tools for conservation management has come forward in leaps and bounds. Once considered a ‘nice to have’, genetic data are fast becoming an essential tool for informing and managing translocations. However, due to the complexity of the field, easily using genetic data for decision-making and monitoring remains beyond the reach of most managers and conservation biologists. In May 2020, we launched the Threatened Species Initiative (TSI), a programme designed to generate genomic resources for Australia’s threatened species. Critical to the project is not only the generation of reference genomes and population genetic data but an online toolkit for conservation managers. The toolkit is a ‘one stop shop’ from collecting samples, to generating and analysing genetic data, to an easily interpretable genetic management report. A series of workflows and pipelines have been developed, including the TSI Biodiversity Portal, that uses point and click web interfaces to easily transfer raw sequence data and assemble genomes, transcriptomes and soon population genetics for management decisions. Here we present how the current toolkit works and provide case study examples for how it is being used to inform translocations and the management of threatened species.

Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II

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Type: Journal article

Reference: Luke W Silver, Carolyn J Hogg, Katherine Belov, Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II, Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae156, https://doi.org/10.1093/gbe/evae156

Abstract

The major histocompatibility complex (MHC) plays a vital role in the vertebrate immune system due to its role in infection, disease and autoimmunity, or recognition of “self”. The marsupial MHC class II genes show divergence from eutherian MHC class II genes and are a unique taxon of therian mammals that give birth to altricial and immunologically naive young providing an opportune study system for investigating evolution of the immune system. Additionally, the MHC in marsupials has been implicated in disease associations, including susceptibility to Chlamydia pecorum infection in koalas. Due to the complexity of the gene family, automated annotation is not possible so here we manually annotate 384 class II MHC genes in 29 marsupial species. We find losses of key components of the marsupial MHC repertoire in the Dasyuromorphia order and the Pseudochiridae family. We perform PGLS analysis to show the gene losses we find are true gene losses and not artifacts of unresolved genome assembly. We investigate the associations between the number of loci and life history traits, including lifespan and reproductive output in lineages of marsupials and hypothesize that gene loss may be linked to the energetic cost and tradeoffs associated with pregnancy and reproduction. We found support for litter size being a significant predictor of the number of DBA and DBB loci, indicating a tradeoff between the energetic requirements of immunity and reproduction. Additionally, we highlight the increased susceptibility of Dasyuridae species to neoplasia and a potential link to MHC gene loss. Finally, these annotations provide a valuable resource to the immunogenetics research community to move forward and further investigate diversity in MHC genes in marsupials.