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Sub-publications- Oskars, T.R., Bouchet, P. & Malaquias, M.A.E. 2015. A new phylogeny of the Cephalaspidea (Gastropoda: Heterobranchia) based on expanded taxon sampling and gene markers. Molecular Phylogenetics and Evolution 89: 130-150
- Oskars, T.R. & Malaquias, M.A.E. 2019. A molecular phylogeny of the Indo-West Pacific species of Haloa sensu lato gastropods (Cephalaspidea: Haminoeidae): Tethyan vicariance, generic diversity, and ecological specialization. Molecular Phylogenetics and Evolution 139(106557)
- Owen, C.L., Marshall, D.C., Hill, K.B.R. & Simon, C. 2015. The phylogenetic utility of acetyltransferase (ARD1) and glutaminyl tRNA synthetase (QtRNA) for reconstructing Cenozoic relationships as exemplified by the large Australian cicada Pauropsalta complex. Molecular Phylogenetics and Evolution 83: 258-277
- Palm, H.W., Waeschenbach, A. & Littlewood, D.T.J 2009. Molecular phylogeny and evolution of the Trypanorhyncha Diesing, 1863 (Platyhelminths: Cestoda). Molecular Phylogenetics and Evolution 52: 351-367
- Parkin, T., Donnellan, S.C., Parkin, B., Shea, G.M. & Rowley, J.J.L. 2023. Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia). Molecular Phylogenetics and Evolution 189: 107934
- Paton, T.A., Baker, A.J., Groth, J.G. & Barrowclough, G.F. 2003. RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Molecular Phylogenetics and Evolution 29: 268-278
- Patterson, S.A., Morris-Pocock, J.A. & Friesen, V.L. 2011. A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes). Molecular Phylogenetics and Evolution 58(2): 181–91
- Pavón-Vázquez, C.J., Esquerré, D., Fitch, A.J., Maryan, B., Doughty, P., Donnellan, S.C. & Keogh, S.J. 2022. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Molecular Phylogenetics and Evolution 173(107516): 1-19
- Pepper, M., Barquero, M.D., Whiting, M.J. & Keogh, J.S. 2014. A multi-locus molecular phylogeny for Australia's iconic Jacky Dragon (Agamidae: Amphibolurus muricatus): Phylogeographic structure along the Great Dividing Range of south-eastern Australia. Molecular Phylogenetics and Evolution 71: 149-156
- Pepper, M., Doughty, P., Hutchinson, M.N. & Keogh, J.S. 2011. Ancient drainages divide cryptic species in Australia's arid zone: Morphological and multi-gene evidence for four new species of Beaked Geckos (Rhynchoedura). Molecular Phylogenetics and Evolution 61: 810-822
- Pepper, M., Doughty, P. & Keogh, J.S. 2006. Molecular phylogeny and phylogeography of the Australian Diplodactylus stenodactylus (Gekkota, Reptilia) species-group based on mitochondrial and nuclear genes reveals an ancient split between Pilbara and non-Pilbara D. stenodactylus. Molecular Phylogenetics and Evolution 41: 539-555
- Perez, K.E., Ponder, W.F., Colgan, D.J., Clark, S.A. & Lydeard, C. 2005. Molecular phylogeny and biogeography of springassociated hydrobiid snails of the Great Artesian Basin, Australia. Molecular Phylogenetics and Evolution 34: 545-556
- Perez-Losada, M., Ricoy, M., Dominguez, J. & Marshall, J. 2009. Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution 52: 293-302
- Petersen, F.T., Meier, R., Kutty, S.N. & Wiegmann, B.M. 2007. The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers. Molecular Phylogenetics and Evolution 45(1893–94): 111–122
- Plazzi, F. & M. Passamontia 2010. Towards a molecular phylogeny of Mollusks: Bivalves' early evolution as revealed by mitochondrial genes. Molecular Phylogenetics and Evolution 57(2): 641-657
- Podar, M., Haddock, S.H.D., Sogin, M. & Harbison, G.R. 2001. A molecular phylogenetic framework for phylum Ctenophora using 18S rRNA genes. Molecular Phylogenetics and Evolution 21: 218-230
- Pola, M. & Gosliner, T.M. 2010. The first molecular phylogeny of cladobranchian opisthobranchs (Mollusca, Gastropoda, Nudibranchia). Molecular Phylogenetics and Evolution 56: 931-941
- Poore, G.C.B. & Andreakis, N. 2011. Morphological, molecular and biogeographic evidence support two new species in the Uroptychus naso complex (Crustacea: Decapoda: Chirostylidae). Molecular Phylogenetics and Evolution 60(1): 152-169
- Porter, M.L., Pérez-Losada, M. & Crandall, K.A. 2005. Modelbased multi-locus estimation of decapod phylogeny and divergence times. Molecular Phylogenetics and Evolution 37: 355-369
- Puckridge, M., Last, P.R. & Andreakis, N. 2015. The role of peripheral endemism and habitat associations in the evolution of the Indo-West Pacific tuskfishes (Labridae: Choerodon). Molecular Phylogenetics and Evolution 84: 64-72
- Puslednik, L. & Serb, J.M. 2008. Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Molecular Phylogenetics and Evolution 48: 1178-1188
- Pyron, R.A., Burbrink, F.T., Colli, G.R., Montes de Oca, A.N., Vitt, L.J., Kuczynski, C.A. & Wiens, J.J. 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Molecular Phylogenetics and Evolution 58(2): 329–342 [Date published online 11 Nov 2010]
- Pyron, R.A. & Wiens, J.J. 2011. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of advanced frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61: 543–583
- Quenouille, B., Bermingham, E. & Serge Planes, S. 2004. Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution 31: 66–88
- Rabosky, D.L., Hutchinson, M.N., Donnellan, C.C., Talaba, A.L. & Lovette, I.J. 2014. Phylogenetic disassembly of species boundaries in a widespread group of Australian skinks (Scincidae: Ctenotus). Molecular Phylogenetics and Evolution 77: 71–82
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