ACAD Recent Publications

2008 2007 2006 2005 2004 2003

2009

• Sands, CJ, Lancaster ML, Austin JJ, Sunnucks P (2009) Single copy nuclear DNA markers for the onychophoran Phallocephale tallagandensis Conservation Genetics Resources DOI 10.1007/s12686-009-9004-0

• Roberts M, Goldsworthy SD, Page B, Steer M, Austin JJ (2009) Assessment of morphological and molecular diet analysis techniques: application of a combined approach to resolve the diet of arrow squid, Nototodarus gouldi, in the eastern Great Australian Bight. Molecular Ecology Resources (accepted June 2009)

•  Austin JJ, Arnold EN, Jones CG (2009) Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial and nuclear gene sequences. Zootaxa (accepted 4/4/2009)

• Barnett, R., Shapiro, B., Barnes, I., Ho SYW., Burger, J., Yamaguchi, N., Higham, T., Wheeler, HT., Rosendahl, W., Sher, AV., Sotnikova, MV., Kuznetsova, T., Baryshnikov, GF., Martin, LD., Harington, CR., Burns, J., Cooper, A. Phylogeography of lions (Panthera leo) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology

• Boessenkool, S., Austin, J. J., Worthy, T. H., Scofield, P., Cooper, A., Seddon, P. J. & Waters, J. M. 2009. Relict or colonizer? Extinction and range expansion of penguins in southern New Zealand. Proceedings of the Royal Society B doi:10.1098/rsbp.2008.1246

2008

• Stewart, JR, Cooper, A. Ice Age refugia and Quaternary extinctions: An issue of Quaternary evolutionary palaeoecology. Quat Sci Reviews. doi:10.1016/j.quascirev.2008.10.005

• Gongora, J., Rawlence, NJ., Mobegi, VA., Jianlin, H., Alcalde, JA., Matus, JT., Hanotte, O., Moran, C., Larson, G., Austin, JJ., Ulm, S., Cooper, A. More DNA and dating studies needed for ancient El-Arenal-1 chickens. PNAS (in press, Nov 2008)

• Boessenkool, S., Austin JJ., Worthy TH., Scofield, P., Cooper A., Seddon, PJ., Waters, JM. Relict or colonizer? Extinction and range expansion of penguins in southern New Zealand. Proceedings Royal Society Biology (in press, Nov 2008)

• Wood, JR., Rawlence, NJ., Rogers, GM., Austin, JJ., Worthy, TH., Cooper, A. Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes). Quat. Sci. Rev. doi:10.1016/j.quascirev.2008.09.019

• Krause, J., Unger., T., Nocon, A., Kolokotronis, SO., Slatkin, M., Paabo, S., Hofreiter M., Bray, S., Cooper., A., et al (2008), 'Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary (pdf 662kB)', BMC Evolutioarny Biology. doi 10.1186/1471-2148-8-220

• Orlando, L., Male, D., Alberdi, MT., Prado, JL., Prieto, A., Cooper, A., & Hanni, C., Ancient DNA Clarifies the Evolutionary History of American Late Pleistocene Equids. (pdf 248kB) Journal of Molecular Evolution. doi 10.1007/s00239-008-9100-x (2008)

• Gongora, J., Rawlence, N.J., Mobegi, V.A., Jianlin, H., Alcalde, J.A., Matus, J.T., Hanotte, O., Moran, C., Larson, G., Austin, J., Ulm, S., Cooper, A., Indo-European and Asian origins for modern Chilean and Pacific archaeological chickens revealed by mtDNA. Proceedings of the National Academy of Science USA doi 105:10308-10313

• Zalloua, PA., Platt, DE., El Sibai, M., Khalife, J., Makhoul, N., Haber, M., Xue, Y., Izaabel, H., Bosch, E., Adams, SM., Arroyo, E., López-Parra, AM., Aler, M., Picornell, A., Ramon, M., Jobling, MA., Comas, D., Bertranpetit, J., Wells, RS., Tyler-Smith, C. The Genographic Consortium. Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean. American Journal Human Genetics. PMID: 18976729 (2008).

• Behar, DM., Blue-Smith, J., Soria-Hernanz, DF., Tzur, S., Hadid, Y., Bormans, C., Moen, A., Tyler-Smith, C., Quintana-Murci, L., Wells RS. The Genographic Consortium. A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals. Hum Mutat. PMID: 18629826 (2008)

• Behar, DM., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R., Makkan, H., Tzur, S., Comas, D., Bertranpetit, J., Quintana-Murci, L., Tyler-Smith, C., Wells, RS., Rosset, S. The Genographic Consortium. The dawn of human matrilineal diversity. American Journal Human Genetics. 82:1130-40. (2008)

• Zalloua, PA., Xue, Y., Khalife, J., Makhoul, N., Debiane, L., Platt, DE., Royyuru, AK., Herrera, RJ., Hernanz, DF., Blue-Smith, J., Wells, RS., Comas, D., Bertranpetit, J., Tyler-Smith, C. The Genographic Consortium. Y-chromosomal diversity in Lebanon is structured by recent historical events. American Journal Human Genetics. 82:873-82 (2008)

• Gan, RJ., Pan, SL., Mustavich, LF., Qin, ZD., Cai, XY., Qian, J., Liu, CW., Peng, JH., Li, SL., Xu, JS., Jin, L., Li, H. The Genographic Consortium. Pinghua population as an exception of Han Chinese's coherent genetic structure. American Journal Human Genetics. 53:303-13 (2008)
  

• Parida, L., Melé, M., Calafell, F., Bertranpetit, J. The Genographic Consortium. Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns. Journal Computer Biology 15:1133-54. PMID: 18844583 (2008)

• Shoo, L.P., Rose, R., Doughty, P., Austin, J.J., Melville, J., (in press) Diversification patterns of pebble-mimic dragons are consistent with historical disruption of important habitat corridors in arid Australia. Molecular Phylogenetics and Evolution

• Nicholls, J.A., Austin, J.J., Pavlacky, D.C., & Green, D.C., (2007) Characterization of polymorphic microsatellites in the logrunner, Orthonyx temminckii (Aves: Orthonychidae). Molecular Ecology Notes 7:1117-1119

• Worthy, T. H; Lee, M. S. Y. 2008. Affinities of Miocene (19-16 Ma) waterfowl (Anatidae: Manuherikia, Dunstanetta and Miotadorna) from the St Bathans Fauna, New Zealand. Palaeontology 51(3): 677-708. doi: 10.1111/j.1475-4983.2008.00778.x.

• Wood, J.R., Worthy, T.H., Rawlence, N.J., Jones, S.M., Holdaway, R.N., Read, S.E. 2008. A deposition mechanism for Holocene miring bone deposits, South Island, New Zealand. Journal of Taphonomy 6: 1-20.

• Wilmshurst, J. M.; Anderson, A. J.; Higham, T. F. G.; Worthy, T. H. 2008. Dating the late prehistoric dispersal of Polynesians to New Zealand using the commensal Pacific rat. Proceeding of the National Academy of Sciences 105(22): 7676-7680.

• Holdaway, R.N.; Worthy, T.H., 2008. The Late Quaternary avifauna. Pp, 445-492, in Winterbourn, M. J., Knox, G. A., Burrows C. J. & Marsden, I. D. (eds), The natural history of Canterbury, 3rd edition. Canterbury University Press, Christchurch, 926 pp. (Book Chapter)

• Worthy, T. H.; Tennyson, A. J. D.; Hand, S. J.; Scofield R. P. 2008. A new species of the diving duck Manuherikia and evidence for geese (Aves: Anatidae: Anserinae) in the St Bathans Fauna (Early Miocene), New Zealand. Journal of the Royal Society of New Zealand 38(2): 97-114.

• Worthy, T. H.; Wragg, G. M. 2008. A new genus and species of pigeon (Aves: Columbidae) from Henderson Island, Pitcairn Group. Pp 499-510, in: Clark, G., Leach, F., O’Connor, S. (eds), Terra Australis 2. Islands of Inquiry: Colonisation, seafaring and the archaeology of maritime landscapes. ANU E Press, The Australian National University, Canberra. 510 pp.

• Worthy, T. H. 2008. Pliocene waterfowl (Aves: Anseriformes) from South Australia and a new genus and species. Emu 108: 153-165.

• Wood, J.R., Rawlence, N.J., Rogers, G, Austin, J, Cooper, A., Worthy, T.H., 2008. Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moas (Aves, Dinornithiformes). Quaternary Science Reviews 27: 2593-2602.

• Worthy, T. H.; Olson, S. L.; Smith T. 2008. A reassessment of the fossil goose Anser scaldii Lambrecht, 1933 (Aves: Anatidae). Bulletin of the British Ornithologist’s Club 128(4): 228-232.

2007

• Larson, G., Albarella, U., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J-D., Edwards, C.J., Schlumbaum, A., Dinu, A., Balacsescu, A., Dolman, G., Tagliacozzo, A., Manaseryan, N., Miracle, P., Van Wijngaarden-Bakker, L., Masseti, M., Bradley, D.G. & Cooper, A., Ancient DNA, pig domestication, and the spread of the neolithic into Europe. Proceedings National Academy of Sciences 13(48) (2007)

• Brotherton, P., Endicott, P., Sanchez, J.J., Beaumont, M., Barnett, R., Austin, J., Cooper., A., Novel high-resolution characterization of ancient DNA reveals C>U-type base modification events as the sole cause of post mortem miscoding lesions, (pdf 252kB) Nucleic Acids Research.doi 10.1093/nar/gkm588 (2007)

• Kowalchuk GA, Austin JJ, Gooding PS & Stephen JR (2007) Valid Recovery of Nucleic Acid Sequence Information from High Contamination Risk Samples – Ancient DNA and Environmental DNA. In: Perspectives in Bioanalysis, Volume 2 - New High Throughput Technologies for DNA Sequencing and Genomics (ed. K. Mitchelson), Macmillan

• Larson, G., Cucci, T., Fujita, M., Matisoo-Smith, E., Robins, J., Anderson, A., Rolett, B., Spriggs, M., Dolman, G., Kim, TH., Thuy, N. T.D., Randi, E., Doherty, M., Due, R. A., Bollt, R., Djubiantono, T., Griffin, B., Intoch, M., Keane, E., Kirch, P., Li, K.T., Morwood, M., Pedrina, L.M., Piper, PJ., Rabett, R.J., Shooter, P., Van den Bergh, G., West, E., Wickler, S., Yuan, J., Cooper, A., and Dobney, K. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania. Proceedings National Academy of Sciences 104(12) 4834-9 (2007)

• Ho SYW, Shapiro S, Phillips MJ, Cooper A, Drummond AJ. Evidence for time dependency of molecular rate estimates Systematic Biology 56:515-522 (2007).
  

• Behar, D.M., Rosset, S., Blue-Smith, J., Balanovsky, O., Tzur, S., Comas, D., Mithcell., Quintana-Murci, L, Tyler-Smith, C., Wells, R.S., The Genographic Consortium. The Genographic Project Public Participation Mitochondrial DNA Database (pdf 450kB), PloS Genetics 3(6) (2007).

• Melville J, Goebel S, Starr C, Keogh JS & Austin JJ (2007) Conservation genetics and species status of an endangered Australian dragon, Tympanocryptis pinguicolla (Reptilia: Agamidae). Conservation Genetics 8:185-198)

• Doughty P, Maryan B, Austin JJ & Melville J (2007) Independent evolution of salt lake specialization in the genus Ctenophorus (Lacertilia: Agamidae), with a description of a new species from Lake Disappointment, Western Australia. Herpetology 63:72-86

2006

• Endicott P, Metspalu M, Stringer C, Macaulay V, Cooper A, Sanchez J. Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PLoS One 1, e81 (2006).

• Cooper A, Year of the mammoth. PLoS Biology 4, e78 (2006).

• Barnett R, Yamaguchi N, Barnes I, Cooper A. The origin, current diversity and future conservation of the modern lion  (pdf 430kB)(Panthera leo). Proceedings of Royal Society, Biology 273, 2159-2168. (2006).

• Barnett R, Yamaguchi N, Barnes I, Cooper A. Lost populations and preserving genetic diversity in the lion Panthera leo; Implications for its ex situ conservation. Conservation Genetics 7, 507-514 (2006).

• Nicholls JA, Austin JJ, Moritz C & Goldizen AW (2006) Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus. Evolution 60: 1279-1290.

• Austin, JJ & Arnold, EN (2006) Using ancient and recent DNA to explore relationships of extinct and endangered Leiolopisma skinks (Reptilia: Scincidae) in the Mascarene islands. Molecular Phylogenetics and Evolution 39: 503-511.

• Austin, JJ & Melville, J (2006) Incorporating historical museum specimens into molecular systematic and conservation genetics research. Molecular Ecology Notes 6: 1089-1092.

• Austin, JJ, Rose, RJ & Melville, J (2006) Polymorphic microsatellite markers in the painted dragon lizard, Ctenophorus pictus. Molecular Ecology Notes 6:194-196

• Wragg, G. M., Worthy, T. H. (2006). A new species of extinct imperial pigeon (Ducula: Columbidae) from Henderson Island, Pitcairn Group. Historical Biology 18(2): 127-140.

• Holdaway, R. N., Worthy, T. H., (2006). Evolution of New Zealand and its vertebrates. Chapter 6 In Merrick, J. Archer, M., Hickey, G. M., and Lee, M. S. Y. (eds). Evolution and Biogeography of Australasian Vertebrates, Auscipub Pty Ltd: Sydney, Pp 111-128.
  

2005

• Gilbert MTP, Shapiro B, Drummond A, Cooper A. Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondria DNA (pdf 223kB). Journal of Archaeologyical Science 32:1053-1060 (2005).

• Ho SYW, Phillips MJ, Drummond AJ, Cooper A. Accuracy of rate estimation using relaxed clock models with a critical focus on the early metazoan radiation. (pdf 298kB) Society for Molecular Biology and Evolution 22, 1355-1363 (2005).

• Barnett R, Phillips MJ, Martin LD, Harington CR, Leonard JA, Cooper A., Evolution of the extinct sabre-tooths and the American cheetahlike cat. (pdf 46kB) Current Biology 15: R1-R2 (2005).

• Ho SYW, Phillips MJ, Cooper A, Drummond AJ., (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. (pdf 178kB) Society for Molecular Biology and Evolution 22, 1561-1568.

• Weinstock J, Willerslev E, Sher A, Tong W, Ho SYW, Rubenstein R, Storer J, Martin L, Bravi C,Prieto A, Froese D, Scott E, Xulong L, Cooper A. Evolution, systematics, and phylogeography of Pleistocene horses in the new world: A molecular perspective. (pdf 350kB) PLoS Biol 3(8): e241 (2005).

• Larson G, Dobney K, Albarella U, Fang M, Matisoo-Smith L, Robins J, Lowden S, Finlayson H, Brand T, Willerslev E, Rowley-Conwy P, Andersson L, Cooper A. Worldwide phylogeography of wild boar reveals multiple centres of pig domestication (pdf 174kB). Science 307, 1618-1621 (2005).

• Bunce M, Szulkin M, Lerner HRL, Barnes I, Shapiro B, Cooper A, Holdaway RN. Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle (pdf 240kB). PLoS Biology, 3:1-4 (2005).

• Willerslev E, Cooper A. Ancient DNA (pdf 239kB). Review Paper. Proc Roy Soc Lon B. 272:3-16 (2005).

• Nicholls, JA & Austin, JJ (2005) Phylogeography of an east Australian wet forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA and morphology. Molecular Ecology 14, 1485-1496.

• Rheindt, FE & Austin, JJ (2005) Major analytical and conceptual short-comings in a recent taxonomic revision of the Procellariiformes - a reply to Penhallurick and Wink (2004). Emu 105, 181-186.

• Beadell, JS, Gering, E, Austin, JJ, Dumbacher, JP, Pierce, MA, Pratt, TK, Atkinson, CT & Fleischer, RC (2005) Host-specificity and prevalence of avian malaria parasites in the Austral-Papuan region. Molecular Ecology 13, 3829-3844.

• Bardeleben, C, Semple-Delaney, K, Austin, JJ & Moore, RL (2005) Isolation of polymorphic tetra-nucleotide microsatellite markers for the grey-headed robin Poecilodryas albispecularis. Molecular Ecology Notes 5, 146-148.

• Bardeleben, C, Gray, MM, Austin, JJ & Amorim do Rosario, I (2005) Isolation of polymorphic tetra-nucleotide microsatellite markers for the large-billed scrubwren Sericornis magnirostris. Molecular Ecology Notes 5, 143-145.

• Bardeleben, C, Moore, RL, Austin, JJ & Robson, T (2005) Isolation of polymorphic tetra-nucleotide microsatellite markers for the Satin Bowerbird Ptilonorhynchus violaceus. Molecular Ecology Notes 5, 305-307.

2004

• Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, AV Sher, Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC,Froese DG, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, and Cooper A. Rise and fall of the Beringian steppe bison (pdf 2MB). Science 306:1561-1565 (2004).

• Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TFG, Richards MP, O'Connell TC, Tobin DJ, Janaway RC, and Cooper A. Ancient mitochondrial DNA from hair (pdf 72kB). Current Biology 14:R463-R464 (2004).

• Cooper A, Drummond AJ, and Willerslev E. Ancient DNA: Would the real Neandertal please stand up? (pdf 67kB) Curr. Biol. 14:R431-433 (2004).

• Strugnell J, Norman M, Drummond AJ, and Cooper A. Neotenous origins for pelagic octopuses (pdf 1MB). Curr. Biol. 14:R300-R301 (2004).

• Gilbert MTP, Cuccui J, White W, Lynnerup N, Titball RW, Cooper A, Prentice MB. Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims (pdf 177kB). Microbiology 150: 341-354 (2004).

• Willerslev E, Hansen AJ, Rönn R, Brand TB, Barnes I, Wiuf C, Gilichinsky D,Mitchell D, Cooper A. Long-term survival of bacterial DNA (pdf 98kB) Curr.Biol. 14:R9-10 (2004).

• Austin, JJ, Bretagnole, V & Pasquet, E (2004) A global molecular phylogeny of the small Puffinus shearwaters and implications for the systematics of the Little/Audubon's shearwater complex. Auk 121, 847-864.

• Austin, JJ, Arnold, EN & Jones, CG (2004) Reconstructing an island radiation using ancient and recent DNA: the extinct and living geckos (Phelsuma) of the Mascarene islands. Molecular Phylogenetics and Evolution 31, 109-122.

• Cook, CE, Austin, JJ, and Disney, RHL (2004) A mitochondrial 12S and 16S rRNA phylogeny of critical genera of the Phoridae (Diptera) and related families of Aschiza. Zootaxa 593, 1-11.

2003

• Gilbert MTP, Willerslev E, Hansen A, Barnes I, Rudbeck L, Lynnerup N, Cooper A., Characterisation of genetic miscoding lesions caused by post-mortem damage (pdf 187kB). Am. J. Hum. Genet. 72:48-61, (2003).

• Gilbert MTP, Willerslev E, Hansen A, Barnes I, Rudbeck L, Lynnerup N, Cooper A. Distribution patterns of post-mortem damage in human mitochondrial DNA. Am. J. Hum. Genet. 72:32-47, (2003).

• Jaenicke-Després V, Buckler ES, Smith BD, Gilbert MTP, Cooper A, Doebley J, Pääbo S. Early allelic selection in maize as revealed by ancient DNA (pdf 152kB). Science 302:1206-1208 (2003).

• Bunce M, Worthy TH, Hoppitt W, Ford T, Willerslev E, Drummond A, Cooper A. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis (pdf 438kB). Nature 425:172-175 (2003).

• Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky D, Cooper A. Diverse plant and animal genetic records from Holocene and Pleistocene and sediments (pdf 124kB). Science 300:791-795 (2003).

• Austin, JJ, Arnold, EN & Bour, R (2003) Was there a second adaptive radiation of giant tortoises in the Indian Ocean? Using mitochondrial DNA to investigate speciation and biogeography of Aldabrachelys (Reptilia, Testudinidae) Molecular Ecology 12, 1415-1424