Current research projects

Phylogenomics of a rapid radiation: exon capture of old endemic rodents of Sahul

Co-authors and collaborators: Dr. Kevin Rowe, Dr. Adnan Moussalli, Professor Craig Moritz and the Oz Mammals Genomics Consortium

The old endemic rodents of Sahul (Australia and New Guinea) are approximately 160 species in 37 genera, and are the result of a single over-water colonisation event from southeast Asia ~ 7-9 million years ago. Rapid accumulation of lineages following initial colonisation of Sahul, and subsequent colonisations of present-day mainland Australia and nearby islands, have made phylogenetic relationships in this group particularly difficult to resolve using small numbers of loci. Using a custom exon capture probe set designed as part of my PhD, we aim to resolve a species-level phylogeny of all ~160 Sahulian old endemic Hydromyini using new sequence data from 1200+ genes. These data will enable unprecedented understanding of relationships within this rapid adaptive radiation, forming the basis for macroevolutionary tests of lineage accumulation, diversification rate, biogeographic transitions and divergence dating.

EJ Roycroft et al. (2020) Phylogenomics uncovers confidence and conflict in the rapid radiation of Australo-Papuan rodents. Systematic Biology. [free access link]

JE Deakin, […multiple authors], EJ Roycroft, KJ Travouillon, AR Weeks, J Worthington Wilmer, A Young, R Johnson, C Moritz (In revision). Oz Mammals Genomics initiative: Developing genomic resources for Australian mammals.

This project is funded by BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).

Resurrecting the dead: museum genomics of extinct Australian rodents

Co-authors and collaborators: Dr. Kevin Rowe, Dr. Adnan Moussalli, Professor Craig Moritz and the Oz Mammals Genomics Consortium

The rate of recent mammalian extinction in Australia is the worst in the world. Of these, native Australian rodents have been disproportionately affected, with 12 out of ~60 species now officially listed as extinct. Nine of these species have been historically collected from live individuals, and are preserved in Australian and international museum collections. The last collection date for the majority of these species ranges from ~1870 – ~1915, with the Bramble Cay melomys most recently declared extinct in 2019. Using NGS approaches applied to historically collected museum specimens, this project aims to generate a combination of exon capture and whole-exome sequence data from all recently extinct Australian endemic rodents, to understand the diversity lost to recent extinction as a direct result of human impact.

E Roycroft et al. (In press) Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement. TBA

Photo: Kevin C. Rowe, Old Endemic rodents of Sahul

This project is funded by the Alfred Nicholas Fellowship (to EJR), the Museums Victoria 1854 scholarship (to EJR), and BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).

Genomics of Gehyra geckos

Collaborators: Professor Craig Moritz and the Australian Reptile and Amphibian Genomics (AusARG) Consortium

The genus Gehyra represents a major radiation among Australian lizards and a subject of studies in chromosome change, speciation, adaptive evolution and sex chromosome evolution for 40 years. Recent phylogenomic and taxonomic studies have resolved species boundaries and relationships among the 62 lineages (49 described species).

This project will generate high-quality reference genomes from four species; Gehyra moritzi, G. purpurascens, G. lapistola and G. paranana. Using these genomes as anchor points across the phylogeny, this project will then examine comparative genomics, chromosome evolution and historical demography across the Australian Gehyra radiation.

This project is funded by the AusARG consortium, and the Australian Research Council.

Photo: Sam Gordon, Gehyra purpurascens

Phylogeography and population genomics of a continental clade: the cryptic delicate mouse complex

Co-authors and collaborators: Dr. Phoebe Burns, Professor Bill Breed, Dr. Fred Ford, Dr. Kevin Rowe, Dr. Adnan Moussalli, Professor Craig Moritz and the Oz Mammals Genomics Consortium

The delicate mouse complex (Pseudomys delicatulus, P. novaeholladiae, P. hermannsbergensis, P. bolami) is a continentally distributed native Australian rodent clade. Fluctuating climates during the Pleistocene have driven extensive undocumented diversity in the delicate mice. Undefined species are problematic for conservation assessment, as species cannot be protected if they are not identified and classified. To quantify this cryptic diversity, this project uses a combined molecular and morphological approach, using exon capture sequence data and 3D micro-CT scanning to understand evolution of delicate mice in Australia.

This project is funded by the Native Australian Animals Trust (to EJR), grants from the Holsworth Wildlife Research Endowment to both EJR and PB, Zoos Victoria funding to PB, and by BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).

Photo: Phoebe A. Burns, Pseudomys delicatulus

Past projects

Genomics of adaptive evolution and convergence in murine rodents

Co-authors and collaborators: Dr. Kevin Rowe, Dr. Adnan Moussalli, Assistant Professor Jake Esselstyn and Associate Professor Jeff Good

Adaptive radiations are characterised by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialisation may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialisation (including phenotypic convergence) are correlated with shared signatures of molecular evolution.

Using whole exome sequencing, we examined how molecular evolution is correlated with diversification in the spectacular adaptive radiation of murine rodents.

E Roycroft et al. (2021) Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents. Genome Biology and Evolution.

Photos: Kevin C. Rowe , Paucidentomys vermidax

This project was funded by NSF grant DEB-1754096 and DEB-1754393: ‘Rates of lineage, phenotypic, and genomic diversification in replicated radiations of murine rodents’.

Environmental correlates to parallel trait evolution in Australian rodents

Collaborators: Jon Nations and Kevin Rowe

Closely related species that occur across steep environmental gradients often display clear phenotypic differences, and examining these patterns is crucial to understanding how environmental variation shapes diversity. Australia encompasses a striking array of biomes, ranging from vast deserts to tropical rainforests. The Australian endemic Pseudomys Division (Muridae: Murinae) has repeatedly colonised arid, monsoon, and temperate mesic biomes over the last 5 million years. Using occurrence data, trait data, and Bayesian phylogenetic multilevel modelling we examined the relationship between phenotype and environment in the Pseudomys Division. Understanding the flexibility of key functional traits at short evolutionary timescales provides insight into the adaptability of organisms in the face of future changing environments.

EJ Roycroft et al. (2020) Environment predicts repeated body size shifts in a recent radiation of Australian mammals. Evolution.