- Brown, S., Clarke, M.F. and Clarke, R.H. (2009) Fire is a Key Element in the Landscape-scale Habitat Requirements and Global Population Status of a Threatened Bird: the Mallee Emu-wren (Stipiturus mallee). Biological Conservation 142: 432-445.
- Ewen, J.G., Ciborowski, K., Clarke, R.H., Boulton, R.L., & Clarke, M.F. (2008) Evidence of extra-pair paternity in two socially monogamous Australian passerines: the crescent honeyeater and the yellow-faced honeyeater. Emu 108: 133-108.
- Clarke, R.H., Boulton, R.L. and Clarke, M.F. (2005) Estimating population size of the black-eared miner, with an assessment of landscape-scale habitat requirements. Pacific Conservation Biology 11: 174-188.
- Clarke, R.H. and Schultz, M. (2005) Land-based observations of seabirds from Sub-Antarctic Macquarie Island during 2002 and 2003. Marine Ornithology 33: 7-17.
- Mustoe, S and Clarke, R.H. (2004) Mallee Emu-wren, sparking concern in the Victorian mallee. National Environmental Law Review September 2004, 3: 54-58.
- Clarke, R.H. (2004) The avifauna of northern Torres Strait: notes on a wet season visit. Australian Field Ornithology 21: 49-66.
- Clarke, R.H., Schipper, C., Boulton, R.L., Ewen, J.G., and Clarke, M.F. (2004) Biometrics and sexing criteria of the Yellow-faced Honeyeater Lichenostomus chrysops. Corella 27: 106-108.
- Clarke, R.H., Oliver, D.L., Boulton, R.L., Casey, P. and Clarke, M.F. (2003) Assessing programs for monitoring threatened species – a tale of three honeyeaters (Meliphagidae). Wildlife Research 30: 427-435
- Clarke, R.H., Boulton, R.L., Ewen, J.G., Moysey, E. and Clarke, M.F. (2002) Methods for aging and sexing the Black-eared Miner Manorina melanotis and Yellow-throated Miner M. flavigula. Emu 102: 339-334
- Clarke, R.H., Boulton, R.L. and Clarke, M.F. (2002) Translocation of the socially complex Black-eared Miner Manorina melanotis: a trial using hard and soft release techniques. Pacific Conservation Biology 8: 223-234.
- Clarke, R.H., Gordon, I.R., and Clarke, M.F. (2001) Intraspecific phenotypic variability in the black-eared miner (Manorina melanotis); human-facilitated introgression and the consequences for an endangered taxon. Biological Conservation 99: 145-155
- Ewen, J.G, Clarke, R.H., Moysey, E., Boulton, R.L., Crozier, R.H. and Clarke, M.F. (2001) Primary sex ratio bias in an endangered cooperatively breeding bird, the Black-eared Miner, and its implications for conservation. Biological Conservation 99: 137-145.
- Clarke, R.H. and Clarke, M.F. (2000) The breeding biology of the Crescent Honeyeater, Phylidonyris pyrrhoptera, at Wilsons Promontory, Victoria. Emu 100: 115-124
- Clarke, R.H. and Clarke, M.F. (1999) The social organisation of a sexual dimorphic honeyeater – the Crescent Honeyeater Phylidonyris pyrrhoptera, at Wilsons Promontory, Victoria. Australian Journal of Ecology 24: 644-654
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