Phylogenomics across a continent: diversification of Australo-Papuan rodents
Co-authors and collaborators: Kevin Rowe (MV), Adnan Moussalli (MV), Pierre-Henri Fabre (University of Montpellier), Craig Moritz (ANU) 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 and biogeographic history of this group particularly difficult to resolve. As part of this ongoing project, we have generated species-level data from across all ~160 described species and many cryptic lineages in the Hydromyini to investigate diversification, molecular evolution and biogeography of Australian rodents.
E Roycroft et al. (2022) New Guinea uplift opens ecological opportunity across a continent. Current Biology. https://doi.org/10.1016/j.cub.2022.08.021
E 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], E 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).
Reconstructing Australian mammal extinctions with museum genomics
Co-authors and collaborators: Kevin Rowe (MV), Adnan Moussalli (MV), Craig Moritz (ANU) 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. As part of this project, we are using museum genomics to obtain 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. (2021) Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement. PNAS. https://doi.org/10.1073/pnas.2021390118
E Roycroft et al. (2022) Sequence capture from historical museum specimens: maximizing value for population and phylogenomic studies. Front Ecol Evol https://doi.org/10.3389/fevo.2022.931644
Photo: K. Rowe, Old Endemic rodents of Sahul
This project is supported by BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).
Comparative genomics and chromosome evolution in Gehyra geckos
Collaborators: Craig Moritz (ANU), Janine Deakin (University of Canberra), 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).
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).
We are generating 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, we are investigating genome evolution, chromosome rearrangements, introgression, and historical demography across the Australian Gehyra radiation, including whole genome re-sequencing of short-range endemic versus widespread species.
This project is funded by the AusARG consortium, and the Australian Research Council.
Photo: Sam Gordon, Gehyra purpurascens
Phylogeography and conservation genomics of the Australian delicate mice
Co-authors and collaborators: Phoebe Burns (Zoos Victoria), Marissa Parrott (Zoos Victoria), Bill Breed (University of Adelaide), Fred Ford (Department of Defence), Kevin Rowe (Museums Victoria), Adnan Moussalli (Museums Victoria), Craig Moritz (Australian National University) 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 generated currently undescribed 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, and investigate historical biogeography of delicate mice in Australia, this project uses a combined molecular and morphological approach.
We are also focusing on conservation genomics of the pookila (New Holland mouse, P. novaehollandiae) across its range, especially in Victoria – where the species has seen dramatic declines in recent years. Using an approach integrating museum specimens, contemporary tissues and biobanked samples, we are investigating the past and ongoing loss of diversity in this species.
This project is funded by the Native Australian Animals Trust, Holsworth Wildlife Research Endowment, Zoos Victoria, and BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).
Photo: Phoebe A. Burns, Pseudomys delicatulus
Diversification and extinction in the iconic radiation of Australian marsupials
Collaborators: Oz Mammals Genomics Consortium
We are investigating diversification, biogeography and extinction at a continental-scale with species-level sampling of the iconic radiation of Australian marsupials.
More details soon…
This project is funded by BioPlatforms Australia (as part of the Oz Mammals Genomics Initiative).
Photo: Australian Museum, Petrogale xanthopus
Past projects
Genomics of adaptive evolution and convergence in murine rodents
Co-authors and collaborators: Kevin Rowe (Museums Victoria), Adnan Moussalli (Museums Victoria), Jake Esselstyn (Louisiana State University) and Jeff Good (University of Montana)
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. https://doi.org/10.1093/gbe/evab103
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 (Louisiana State University) and Kevin Rowe (Museums Victoria)
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
Emily Roycroft 