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Sub-publications- Baker, A.M., C. Bartlett, S.E. Bunn, K. Goudkamp, F. Sheldon & J.M. Hughes 2003. Cryptic species and morphological plasticity in long-lived bivalves (Unionoida: Hyriidae) from inland Australia. Molecular Ecology 12: 2707-2717
- Baker, C.S., Slade, R.W., Bannister, J.L. et al. 1994. Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaloptera novaeangliae, world-wide whales. Molecular Ecology 3: 313-328
- Beadell, J.S., Gering, E., Austin, J., Dumbacher, J.P., Peirce, M.A., Pratt, T.K., Atkinson, C.T. & Fleischer, R.C. 2004. Prevalence and differential host-specificity of two avian blood parasite genera in the Australo-Papuan region. Molecular Ecology 13: 3829-3844
- Bird, C.E., Holland, B.S., Bowen, B.W. & Toonen, R.J. 2011. Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago. Molecular Ecology 20: 2128–2141
- Carroll, S.P. 2008. Facing change: forms and foundations of contemporary adaptation to biotic invasions. Molecular Ecology 17(1): 361-372
- Clegg, S.M., Hale & Moritz, C. 1998. Molecular population genetics of the red kangaroo (Macropus rufus): mtDNA variation. Molecular Ecology 7: 679-686
- Coleman, R.A., Weeks, A.R. & Hoffmann, A.A. 2013. Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae). Molecular Ecology
- Cooper, S.J.B., Harvey, M.S., Saint, K.M. & Main, B.Y. 2011. Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia. Molecular Ecology 20: 3219-3236
- Crandall, E.D., Frey, M.A., Grosberg, R.K. & Barber, P.H. 2008. Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods. Molecular Ecology 17: 611-626
- Curtis, E.L., Evans, B.S., Taylor, J.J.U. & Jerry, D.R. 2007. Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limits. Molecular Ecology 16(24): 5193-5203
- Dalebout, M.L., Robertson, K.M., Frantzis, A., et al. 2005. Worldwide structure of mtDNA diversity among Cuvier's beaked whales (Ziphius cavirostris); implications for threatened populations. Molecular Ecology 14: 3353-3371
- Dalebout, M.L., van Helden, A., van Waerebeek, K. & Baker, C.S. 1998. Molecular genetic identification of southern hemisphere beaked whales. Molecular Ecology 7: 687-694
- Franck, P., Cameron, E., Good, G., Rasplus, J.-Y. & Oldroyd, B.P. 2004. Nest architecture and genetic differentiation in a species complex of Australian stingless bees. Molecular Ecology 13: 2317-2331
- Franck, P. in Franck, P., Cameron, E., Good, G., Rasplus, J.-Y. & Oldroyd, B.P. 2004. Nest architecture and genetic differentiation in a species complex of Australian stingless bees. Molecular Ecology 13: 2317-2331
- Garrick, R.C., Sands, C.J., Rowell, D.M., Tait, N.N., Greenslade, P. & Sunnucks, P. 2004. Phylogeography recapitulates topography: very fine-scale local endemism of a saproxylic 'giant' sprintail at Tallaganda in the Great Dividing Range of south-east Australia. Molecular Ecology 13: 3315-3330
- Georges, A., Gruber, B., Pauly, G.B., White, D., Adams, M., Young, M.J., Kilian, A., Zhang, X., Shaffer, H.B. and Unmack, P.J. 2018. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia. Molecular Ecology 27: 5195-5213
- Hazliitt, S.L., Eldridge, M.D.B. & Goldizen, A.W. 2004. Strong female philopatry within a brush-tailed rock-wallaby colony in southeast Queensland determined by fine-scale spatial genetic correlation analyses. Molecular Ecology 13: 3621-3632
- Houlden, B.A., England, P.R., Taylor, A.C., Greville, W.D. & Sherwin, W.B. 1996. Low genetic variability of the koala Phascolarctos cinereus in south-eastern Australia following a severe population bottleneck. Molecular Ecology 5: 269-281
- Hughes, J., A.M. Baker, C. Bartlett, S. Bunn, K. Goudkamp & J. Somerville 2004. Past and present patterns of connectivity among populations of four cryptic species of freshwater mussels Velesunio spp. (Hyriidae) in central Australia. Molecular Ecology 13: 3197-3212
- Hurwood D.A. & Hughes J.M. 1998. Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns. Molecular Ecology 7: 1507–1517
- Jaya, F.R., Tanner, J.C., Whitehead, M.R., Doughty, P., Keogh, J.S., Moritz, C.C. & Catullo, R.A. 2022. Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone. Molecular Ecology 31: 4527–4543
- Jones, A.G., Kvarnemo, C., Moore, G.I., Simmons, L.W.& Avise, J.C. 1998. Microsatellite evidence for monogamy and sex-biased recombination in the Western Australian seahorse Hippocampus angustus. Molecular Ecology 7(11): 1497-1505
- Jones, M.E., Paetkou, D., Geffen, E. & Moritz, C. 2004. Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore. Molecular Ecology 13: 2197-2209
- Kearney, M., Blacket, M.J., Strasburg, J.L. & Moritz, C. 2006. Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia. Molecular Ecology 15: 1743-1748
- Kearney, M. & Blacket, M.J. 2008. The evolution of sexual and parthenogenetic Warramaba: a window onto Plio-Pleistocene diversification processes in an arid biome. Molecular Ecology 17: 5257-5275