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. https://doi.org/10.1093/sysbio/syz044 [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).
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
Details coming soon…
Photos: Kevin C. Rowe , Paucidentomys vermidax
This project is funded by NSF grant DEB-1754096 and DEB-1754393: ‘Rates of lineage, phenotypic, and genomic diversification in replicated radiations of murine rodents’.
The generation of data from Australian species was funded by Bioplatforms Australia (through the Oz Mammals Genomics Initiative), the American Society of Mammalogists (Grant-In-Aid of Research to EJR), the Jasper Loftus-Hill Memorial Fund to EJR, the Margaret Catto Scholarship to EJR, the Holsworth Wildlife Research Endowment to EJR, and the Dame Margaret Blackwood Soroptimist Scholarship to EJR.
EJ Roycroft et al. (In prep) Adaptive molecular evolution during the diversification of murine rodents.
Environmental correlates to parallel trait evolution in Australian rodents
Co-authors and collaborators: Jon Nations and Dr. 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. https://doi.org/10.1111/evo.13859
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
Resurrecting the dead: museum genomics of extinct Australian rodents
Co-authors and collaborators: Dr. Kevin Rowe, Dr. Adnan Moussalli, Associate Professor Pierre-Henri Fabre, 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.
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).