Lab: Samuels s128; Phone 9385-3869

Professional Experience

• 2013 - current: Senior Lecturer, School of BABS, UNSW
• 2009-2012: ARC Fellow, Evolution Ecology & Genetics, Research School of Biology,
  The Australian National University
• 2007-2009: Research Fellow, Comparative Genomics Group, Research School of Biological Sciences, The Australian National University
• 2006-2007: Postdoctoral Fellow, ARC Centre for Kangaroo Genomics, Comparative Genomics Group, Research School of Biological Science, The Australian National University
• 2003-2005: Postdoctoral Fellow, Evolutionary Genomics Group, Department of Zoology, Stellenbosch University, Private Bag X1, Matieland, South Africa

Research Contribution

My research centres on better understanding epigenetic regulation of transcription in diverse vertebrate representatives, specifically focussing on sex chromosomes dosage compensation. The ultimate goal is to understand how complex epigenetic silencing mechanisms evolved. During my PhD I focused on the gene content and evolution of marsupial Y chromosomes, and throughout my first postdoc in South Africa I focused on the genomics of Afrotheria (basal eutherian mammals; which include elephant, aardvarks, etc.).

I was awarded an ARC discovery project to further explore the epigenetics of vertebrate dosage compensation. The next stage of vertebrate genomics and epigenetics for my group involves much use of short read sequencing technologies.

I am currently using the Tasmanian devil to develop a technique for sequencing a whole mammal Y chromosome. For a study of dosage compensation in phylogenetically important vertebrate taxa, I have sequenced the transcriptomes from a male and female elephant, along with a male and female opossum. I use ChIP-Seq to examine the chromatin modifications associated with vertebrate dosage compensation. I have ChIP samples being sequenced from the same opossum cell lines that the transcriptomes were sequenced, which will allow me to directly correlate transcription levels with chromatin modifications on a genome wide scale, avoiding problems associated with variation between individuals and tissue type.

Honours & Awards

• ARC Fellowship 2009-2014: Origin and Evolution of Mammalian Dosage Compensation
• May 2007: Invited to present my work on platypus sex chromosomes at the invitation-only US/Australian Joint Workshop on Vertebrate Comparative Genomics
• November 2008: Invited speaker at the Boden Research Conference, Beyond the Platypus Genome
• Referee for international journals Heredity, Molecular Biology and Evolution, Genome Biology, PLoS Genetics, BMC Evolutionary Biology, BMC Molecular Biology, Chromosome Research and Mammalian Genome

Active Research Projects

• Evolution of Mammal Sex Chromosomes
• Marsupial X Chromosome Inactivation
• Monotreme and Bird Dosage Compensation

Publications

Murtagh, V., O'Meally, D., Sankovic, N., Delbridge, M.L., Kuroki, Y., Boore J.L., Toyoda, A., Jordan, K.S., Pask, A.J., Renfree, M.B., Fujiyama, A., Graves, J.A. & Waters, P.D. (2011)
Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution.
Genome Research. 22(3): 498-507.

Livernois, A.M., Graves, J.A. & Waters, P.D. (2011)
The origin and evolution of vertebrate sex chromosomes and dosage compensation.
Heredity (Edinburgh). 108(1): 50-58. doi: 10.1038/hdy.2011.106

Al Nadaf, S., Deakin, J.E., Gilbert, C., Robinson, T.J., Graves, J.A. & Waters, P.D. (2011)
A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation.
Chromosoma. 121(1):71-78.

Renfree, M.B., Papenfuss, A.T., Deakin, J.E., Lindsay, J., Heider, T., Belov, K., Rens, W., Waters, P.D., Pharo, E.A., Shaw, G., Wong, E.S., Lefèvre, C.M., Nicholas, K.R., Kuroki, Y., Wakefield, M.J., Zenger, K.R., Wang, C., Ferguson-Smith, M., Nicholas, F.W., Hickford, D., Yu, H., Short, K.R., Siddle, H.V., Frankenberg, S.R., Chew, K.Y., Menzies, B.R., Stringer, J.M., Suzuki, S., Hore, T.A., Delbridge, M.L., Mohammadi, A., Schneider, N.Y., Hu, Y., O'Hara, W., Al Nadaf, S., Wu, C., Feng, Z.P., Cocks, B.G., Wang, J., Flicek, P., Searle, S.M., Fairley, S., Beal, K., Herrero, J., Carone, D.M., Suzuki, Y., Sugano, S., Toyoda, A., Sakaki, Y., Kondo, S., Nishida, Y., Tatsumoto, S., Mandiou, I., Hsu, A., McColl, K.A., Lansdell, B., Weinstock, G., Kuczek, E., McGrath, A., Wilson, P., Men, A., Hazar-Rethinam, M., Hall, A., Davis, J., Wood, D., Williams, S., Sundaravadanam, Y., Muzny, D.M., Jhangiani, S.N., Lewis, L.R., Morgan, M.B., Okwuonu, G.O., Ruiz, S.J., Santibanez, J., Nazareth, L., Cree, A., Fowler, G., Kovar, C.L., Dinh, H.H., Joshi, V., Jing, C., Lara, F., Thornton, R., Chen, L., Deng, J., Liu, Y., Shen, J.Y., Song, X.Z., Edson, J., Troon, C., Thomas, D., Stephens, A., Yapa, L., Levchenko, T., Gibbs, R.A., Cooper, D.W., Speed, T.P., Fujiyama, A., Graves, J.A., O'Neill, R.J., Pask, A.J., Forrest, S.M. & Worley, K.C. (2011)
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Genome Biology 12(8):R81.

Badenhorst, D., Dobigny, G., Adega, F., Chaves, R., O’Brien, P.C.M., Ferguson-Smith, M.A., Waters, P.D. & Robinson, T.J. (2011)
Chromosomal evolution in Rattini (Muridae, Rodentia)
Chromosome Research. 19(6): 709-727.

Chaumeil, J.*, Waters, P.D.*, Koina, E., Gilbert, C., Robinson, T.J. & Marshall Graves, J.A. (2011)
Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals.
PLoS One. 6(4) e19040: 1-11. *Equal contribution

Al Nadaf, S., Waters, P.D., Koina, E., Deakin, J.E., Jordan, K.S. & Graves, J.A.M. (2010)
Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic.
Genome Biology. 11: R122.   doi:10.1186/gb-2010-11-12-r122

Ezaz, T., Moritz, B., Waters, P.D., Graves, J.A., Georges, A. & Sarre, S.D. (2009)
The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds.
Chromosome Research. 17: 965-973.

Waters, P.D. & Graves, J.A. (2009)
Monotreme sex chromosomes – implications for the evolution of amniote sex chromosomes.
Reproduction Fertility and Development. 21: 943-951.

Delgado, C.L., Waters, P.D., Gilbert, C., Robinson, T.J. & Graves, J.A. (2009)
Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.
Chromosome Research. 17: 917-926.

Delbridge, M.L., Patel, H.R., Waters, P.D., McMillan D.A. & Graves, J.A. (2009)
Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.
Genome Research. 19: 1350-1360.

Mohammadi, A., Delbridge, M.L., Waters, P.D. & Graves, J.A. (2009)
Conservation of a chromosome arm in two distantly related marsupial species.
Cytogenet Genome Research. 124: 147-150.

Deakin, J.E., Koina, E., Waters, P.D., Doherty, R., Patel, V.S., Delbridge, M.L., Dobson, B., Fong, J., Hu, Y., Hurk, C., Pask, A.J., Shaw, G., Smith, C., Thompson, K., Wakefield, M.J., Yu, H., Renfree, M.B. & Graves, J.A. (2008)
Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.
Chromosome Research: 16, 1159-1175.

Gilbert, C., Pace, J.K. & Waters, P.D. (2008)
Target site analysis of RTE1-LA and its AfroSINE(Anc) partner in the elephant genome.
Gene. 425: 1-8.

Wallis, M.C., Waters, P.D., & Graves, J.A. (2008)
Sex determination in mammals-before and after the evolution of SRY.
Cellular and Molecular Life Sciences. 65: 3182-3195.

Warren, W.C., Hillier, L.W., Graves, J.A.M., Birney, E., Ponting, C.P., Grützner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A.T., Yang, S.P., Heger, A., Locke, D., Miethke, P., Waters, P.D.,  Veyrunes, F., Fulton, L., Fulton, B., Graves, T., Wallis, J., Puente, X.S., López-Otín, C., Ordóñez, G.R., Eichler, E.E., Chen, L., Cheng, Z., Deakin, J.E., Alsop, A., Thompson, K., Kirby, P., Papenfuss, A.T.,  Wakefield, M.J., Olender, T., Lancet, D., Huttley, G.A., Smit, A.F.A., Pask, A., Temple-Smith, P., Batzer, M.A., Walker, J.A., Konkel, M.K., Harris, R.S., Whittington, C.M., Wong, E.S.W., Gemmell, N.J., Buschiazzo, E., Vargas Jentzsch, I.M., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Kriegs, J.O., Brosius, J., Murchison, E.P., Sachidanandam, R., Smith, C., Hannon, G.J., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lefèvre, C.M., Sharp, J.A., Nicholas, K.R., Ray, D.A., Kube, M., Reinhardt, R., Pringle, T.H., Taylor, j., Jones, R.C., Nixon, B., Dacheux, J.L., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, M.N., Pohl, C.S., Smith, S.M., Hou, S., Renfree, M.B.,. Mardis E.R. & Wilson, R.K.  (2008)
Genome analysis of the platypus reveals unique signatures of evolution.
Nature. 453: 175-184.

Veyrunes, F.*, Waters, P.D.*, Miethke, P., Rens, W., McMillan, D., Alsop, A.E., Grützner, F., Deakin, J.E., Whittington, C.M., Schatzkamer, K., Kremitzki, C.L., Graves, T., Ferguson-Smith, M.A., Warren, W. & Marshall Graves, J.A. (2008)
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.
Genome Research. 18: 965-973. *Equal contribution.

Deuve, J.L., Bennett, N.C., Ruiz-Herrera, A., Waters, P.D., Britton-Davidian, J. & Robinson, T.J. (2008)
Dissection of a Y-autosome translocation in Cryptomys hottentotus (Rodentia, Bathyergidae) and implications for the evolution of a meiotic sex chromosome chain.
Chromosoma. 177: 211-217.