Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease

Type: Journal Article

Reference: Nelson, H.V., Silver, L., Kovacs, T.G.L. et al. Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease. Immunogenetics 77, 21 (2025). https://doi.org/10.1007/s00251-025-01378-8

Abstract

Small, isolated populations are often vulnerable to increased inbreeding and genetic drift, both of which elevate the risk of extinction. The Bellinger River turtle (Myuchelys georgesi) is a critically endangered species endemic to a single river catchment in New South Wales, Australia. The only extant wild population, along with the breeding program, face significant threats from viral outbreaks, most notably a nidovirus outbreak in 2015 that led to a 90% population decline. To enhance our understanding of genomic characteristics in the species, including genome-wide and functional gene diversity, we re-sequenced, assembled, and analysed 31 re-sequenced genomes for pure M. georgesi (N = 31). We manually annotated the major histocompatibility complex (MHC), identifying five MHC class I and ten MHC class II genes and investigated genetic diversity across both classes in M. georgesi. Our results showed that genome-wide diversity is critically low in pure M. georgesi, contexualised through comparison with opportunistically sampled backcross animals—offspring of F1 hybrids (M. georgesi × Emydura macquarii) backcrossed to pure M. georgesi (N = 4). However, the variation observed within the core MHC region of pure M. georgesi, extending across scaffold 10, exceeded that of all other macrochromosomes. Additionally, no significant short-term changes in either genome-wide or immunogenetic diversity were detected following the 2015 nidovirus outbreak (before; N = 19, after; N = 12). Demographic history reconstructions indicated a sustained, long-term decline in effective population size since the last interglacial period, accompanied by more recent steep declines. These patterns suggested that prolonged isolation and reduced population size have significantly influenced the dynamics of genome-wide diversity. It is likely that contemporary stressors, including the recent nidovirus outbreak, are acting on an already genetically depleted population. This study offers new insights into genome-wide and immune gene diversity, including immune gene annotation data with broader implications for testudines. These findings provide crucial information to support future management strategies for the species.

Holly Nelson

Bilby release

Holly Nelson (PhD Student) worked on how we can use genomics to revolutionise threatened species management. From genome assembly to downstream analyses using whole-genome data, Holly used her work to answer genetic questions on the Bellinger River Snapping Turtle, Koala, and other threatened species. Her work, in partnership with the NSW Governments Saving Our Species program, aimed to create more robust conservation strategies that can be developed and applied together with wildlife managers.

Sydney Science in Instagram: Meet PhD Student Holly Nelson

Meet PhD student Holly Nelson. Her research with the USYD Australian Wildlife Genomics group and NSW Department of Planning and Environment focuses on using genomic data to help provide tools for the management of threatened species, especially the critically endangered Bellinger River snapping turtle.

Watch the full video here: https://www.instagram.com/sydney_science/reel/Cw1FG6-hhD8/

NSW Department of Planning and Environment: Keeping up with the Bellinger River snapping turtle

An article about people working to conserve the critically endangered Bellinger River snapping turtle to learn more about the species and what’s being done to try to protect it. Research to assist recovery of the Bellinger River snapping turtle is ongoing. University of Sydney PhD student Holly Nelson is using whole genome and genetic data to help inform and develop tools for the management of the species.

Find the full article here: https://www.environment.nsw.gov.au/news/keeping-up-with-the-bellinger-river-snapping-turtle