Changing chromosomes: do genomic hotspots drive evolution in an iconic Australian marsupial?

New genomic data resolves the relationships of living rock-wallabies but how their diverse chromosomes evolved still remains a mystery.

Rock-wallabies are medium-sized members of the kangaroo family and one of Australia’s iconic marsupials. Although most marsupials have chromosomes that have changed little in shape and number over millions of years, rock-wallaby chromosomes are highly variable in both number and shape. So far, 23 chromosomally different rock-wallaby populations have been identified, more than any other marsupial group, with many of these changes occurring quite recently in evolutionary time. This extreme diversity in chromosomes is patchily distributed across the tree of life, but the unique biology of rock-wallabies makes them a valuable model to explore how chromosome changes and other genetic mutations interact to produce new species. Understanding how new species form (i.e. speciation) remains one of the biggest questions in biology, as well as understanding the mechanisms driving speciation.

Although early studies clearly identified highly variable chromosomes in rock-wallabies, our analysis of these changes has been hampered by the difficulty in obtaining a solid understanding of relationships amongst the 17 different rock-wallaby species. While previous studies were only able to look at a few genes to try and establish relationships, this study uses the latest technology to target thousands of genes across the genome and has finally resolved the relationships of all living rock-wallaby species. While this has allowed us to map, for the first time, the order and timing of chromosomal rearrangements in rock-wallabies, it has also revealed some fascinating puzzles. For example, it appears that some chromosomes have rearranged a lot! Indeed, some chromosomes have independently rearranged in the same way in different species.

In order to look more closely at the behaviour of individual chromosomes and how that relates to changes in the genome and ultimately speciation, we were able to use the already published tammar wallaby (Notamacropus eugenii) genome to map each of the ~2000 genes we examined to individual rock-wallaby chromosomes. We were able to separate genes on chromosomes that have rearranged and compare them to genes on chromosomes that haven’t rearranged. This has allowed the first insights into how these chromosome differences may have influenced speciation and potentially point to a greater role for the sex-chromosomes than previously suspected.

We also discovered that genes in the mitochondrial DNA showed different patterns amongst species to those in the nuclear DNA. These differences, which had confused previous studies of interrelationships, appear to have resulted from these rock-wallaby species interbreeding on multiple occasions in their evolutionary past.

This exciting study has clearly demonstrated that by combining new cytogenetic (chromosome) and genomic techniques we have been able to gain novel insights into the age old question of the role of chromosomal change in speciation.

This international collaborative project was conducted researchers from the Australian Museum Research Institute, Australian National University, University of Canberra, National Herbarium of New South Wales, Swedish Museum of Natural History and University of Texas. This work would not have been possible without the frozen tissue collection of the Australian Museum Research Institute.

Dr Sally Potter, Research Associate AMRI, Australian National University & Centre for Biodiversity Analysis
Dr Mark Eldridge, Principal Research Scientist, AMRI

More Information

• Potter, S., Bragg, J.G., Blom, M.P.K. Deakin, J.E., Kirkpatrick, M., Eldridge, M.D.B. and Moritz, C. 2017. Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies. Frontiers in Genetics 8:10.