Refereed Papers

14.	Clarke, A. C., Prost, S., Stanton, J.-A. L., White, W. T. J., Kaplan, M. E., Matisoo-Smith, E. A., and The Genographic Consortium. 2014. From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics 15: Article 68. Updates for the A to Z paper are available here.		Open Access
13.	Storey, A. A., Clarke, A. C., Ladefoged, T., Robins, J., and Matisoo-Smith, E. 2013. DNA and Pacific commensal models: applications, construction, limitations, and future prospects. Journal of Island & Coastal Archaeology 8: 37–65. A more easily read version of Table 1 is available here.		Open Access
12.	Saslis-Lagoudakis, C. H., and Clarke, A. C. 2013. Ethnobiology: the missing link in ecology and evolution. Trends in Ecology & Evolution 28: 67–68.		Open Access
11.	Knapp, M., Clarke, A. C.,† Horsburgh, K. A.,† and Matisoo-Smith, E. A. 2012. Setting the stage — building and working in an ancient DNA laboratory. Annals of Anatomy 194: 3–6. † Equal contributors
10.	Stölting, K. N., Clarke, A. C., Meudt, H. M., Blankenhorn, W. U., and Wilson, A. B. 2011. Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system. Molecular Ecology Resources 11: 494–502.
9.	Seelenfreund, D., Clarke, A. C., Oyanedel, N., Piña, R., Lobos, S., Matisoo-Smith, E. A., and Seelenfreund, A. 2010. Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: anthropological, botanical and genetic considerations. New Zealand Journal of Botany 48: 231–247.		Open Access
8.	McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., and Havey, M. J. 2008. Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science 133: 810–818.		Open Access
7.	Holland, B. R.,† Clarke, A. C.,† and Meudt, H. M.† 2008. Optimizing automated AFLP scoring parameters to improve phylogenetic resolution. Systematic Biology 57: 347–366. Suppl. Material † Joint first authors		Open Access
6.	Michel, C., Hicks, B. J., Stölting, K. N., Clarke, A. C., Stevens, M. I., Tana, R., Meyer, A., and van den Heuvel, M. R. 2008. Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) — implications for incipient speciation in island freshwater fish species. BMC Evolutionary Biology 8: Article 49.		Open Access
5.	van den Heuvel, M. R., Michel, C., Stevens, M. I., Clarke, A. C., Stölting, K. N., Hicks, B. J., and Tremblay, L. A. 2007. Monitoring the effects of pulp and paper effluent is restricted in genetically distinct populations of common bully (Gobiomorphus cotidianus). Environmental Science & Technology 41: 2602–2608.
4.	Meudt, H. M., and Clarke, A. C. 2007. Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science 12: 106–117.
3.	Clarke, A. C., Burtenshaw, M. K., McLenachan, P. A., Erickson, D. L., and Penny, D. 2006. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Molecular Biology and Evolution 23: 893–900. Suppl. Material		Open Access
2.	McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., Scheffer, J., Sims, I., van Heusden, S., Shigyo, M., and Havey, M. J. 2006. Genetic mapping of a major gene affecting onion bulb fructan content. Theoretical and Applied Genetics 112: 958–967.
1.	Erickson, D. L., Smith, B. D., Clarke, A. C., Sandweiss, D. H., and Tuross, N. 2005. An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proceedings of the National Academy of Sciences of the United States of America 102: 18315–18320. Support. Info.		Open Access

Book Chapters

2.	Jones, T. L., Clarke, A. C., Cordero, M.-A., Green, R. C., Irwin, G., Klar, K. A., Matisoo-Smith, E. A., Quiróz, D., Ramírez-Aliaga, J. M., Scaglion, R., Storey, A. A., and Weisler, M. I. 2011. Summary and conclusions. In Jones, T. L., Storey, A. A., Matisoo-Smith, E. A., and Ramírez-Aliaga, J. M. (Eds), Polynesians in America: Pre-Columbian Contacts with the New World, pp. 263–276. Rowman & Littlefield: Lanham, Maryland, United States.
1.	Storey, A. A., Clarke, A. C., and Matisoo-Smith, E. A. 2011. Identifying contact with the Americas: a commensal-based approach. In Jones, T. L., Storey, A. A., Matisoo-Smith, E. A., and Ramírez-Aliaga, J. M. (Eds), Polynesians in America: Pre-Columbian Contacts with the New World, pp. 111–138. Rowman & Littlefield: Lanham, Maryland, United States.

Refereed Conference Proceedings

1.

McCallum, J., Pither-Joyce, M., Clarke, A., Kik, C., Van Heusden, S., Jakse, J., and Havey, M. J. 2005. Towards a framework PCR-based map of onion (Allium cepa L.). In Liu, G. (Ed.), Proceedings of the Fourth International Symposium on Edible Alliaceae, Beijing, China, 21–26 April, 2004, pp. 173–178. Acta Horticulturae 688. International Society for Horticultural Science: Leuven, Belgium.

Consortium Papers

If you cannot access a consortium publication, please e-mail me for a copy.

18.	Javed, A.,† Melé, M.,† Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M. G., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., ArunKumar, G., Pitchappan, R., Bertranpetit, J., Calafell, F., Parida, L., and The Genographic Consortium. 2012. Recombination networks as genetic markers in a human variation study of the Old World. Human Genetics 131: 601–613. Supplementals † Equal contributors
17.	Haber, M., Platt, D. E., Ashrafian Bonab, M., Youhanna, S. C., Soria-Hernanz, D. F., Martínez-Cruz, B., Douaihy, B., Ghassibe-Sabbagh, M., Rafatpanah, H., Ghanbari, M., Whale, J., Balanovsky, O., Wells, R. S., Comas, D., Tyler-Smith, C., Zalloua, P. A., and The Genographic Consortium. 2012. Afghanistan’s ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS ONE 7: Article e34288. Support. Info.		Open Access
16.	Behar, D. M., Harmant, C., Manry, J., van Oven, M., Haak, W., Martinez-Cruz, B., Salaberria, J., Oyharçabal, B., Bauduer, F., Comas, D., Quintana-Murci, L., and The Genographic Consortium. 2012. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times. American Journal of Human Genetics 90: 486–493. Suppl. Data		Open Access
15.	Lu, Y., Wang, C., Qin, Z., Wen, B., Farina, S. E., Jin, L., Li, H., and The Genographic Consortium. 2012. Mitochondrial origin of the matrilocal Mosuo people in China. Mitochondrial DNA 23: 13–19. Suppl. Material
14.	Kang, L.,† Lu, Y.,† Wang, C., Hu, K., Chen, F., Liu, K., Li, S., Jin, L., Li, H., and The Genographic Consortium. 2012. Y-chromosome O3 Haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the Eastern Himalayas. Annals of Human Genetics 76: 92–99. Support. Info. † Equal contributors		Open Access
13.	Melé, M., Javed, A., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M. G., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., Pitchappan, R. M., Arunkumar, G., Parida, L., Calafell, F., Bertranpetit, J., and The Genographic Consortium. 2012. Recombination gives a new insight in the effective population size and the history of the Old World human populations. Molecular Biology and Evolution 29: 25–30. Suppl. Data
12.	Jota, M. S., Lacerda, D. R., Sandoval, J. R., Vieira, P. P. R., Santos-Lopes, S. S., Bisso-Machado, R., Paixão-Cortes, V. R., Revollo, S., Paz-Y-Miño, C., Fujita, R., Salzano, F. M., Bonatto, S. L., Bortolini, M. C., Santos, F. R., and The Genographic Consortium. 2011. A new subhaplogroup of Native American Y-chromosomes from the Andes. American Journal of Physical Anthropology 146: 553–559. Support. Info.
11.	Gaieski, J. B., Owings, A. C., Vilar, M. G., Dulik, M. C., Gaieski, D. F., Gittelman, R. M., Lindo, J., Gau, L., Schurr, T. G., and The Genographic Consortium. 2011. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. American Journal of Physical Anthropology 146: 392–405. Support. Info.
10.	Balanovsky, O.,† Dibirova, K.,† Dybo, A., Mudrak, O., Frolova, S., Pocheshkhova, E., Haber, M., Platt, D., Schurr, T., Haak, W., Kuznetsova, M., Radzhabov, M., Balaganskaya, O., Romanov, A., Zakharova, T., Soria Hernanz, D. F., Zalloua, P., Koshel, S., Ruhlen, M., Renfrew, C., Wells, R. S., Tyler-Smith, C., Balanovska, E., and The Genographic Consortium. 2011. Parallel evolution of genes and languages in the Caucasus region. Molecular Biology and Evolution 28: 2905–2920. Suppl. Data † Equal contributors
9.	Yan, S., Wang, C.-C., Li, H., Li, S.-L., Jin, L., and The Genographic Consortium. 2011. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics 19: 1013–1015. [Corrigendum: Eur. J. Hum. Genet. 2011. 19: 1018. ]
8.	Cai, X.,† Qin, Z.,† Wen, B., Xu, S., Wang, Y., Lu, Y., Wei, L., Wang, C., Li, S., Huang, X., Jin, L., Li, H., and The Genographic Consortium. 2011. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS ONE 6: Article e24282. Support. Info. † Equal contributors		Open Access
7.	Martínez-Cruz, B., Ziegle, J., Sanz, P., Sotelo, G., Anglada, R., Plaza, S., Comas, D., and The Genographic Consortium. 2011. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes. Investigative Genetics 2: Article 13. Additional Material		Open Access
6.	Yang, K., Zheng, H., Qin, Z., Lu, Y., Farina, S. E., Li, S., Jin, L., Li, D., Li, H., and The Genographic Consortium. 2011. Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan. Journal of Human Genetics 56: 253–256. Suppl. Info.
5.	Adler, C. J., Haak, W., Donlon, D., Cooper, A., and The Genographic Consortium. 2011. Survival and recovery of DNA from ancient teeth and bones. Journal of Archaeological Science 38: 956–964. Suppl. Material
4.	Haber, M.,† Platt, D. E.†, Badro, D. A., Xue, Y., El-Sibai, M., Ashrafian Bonab, M., Youhanna, S. C., Saade, S., Soria-Hernanz, D. F., Royyuru, A., Wells, R. S., Tyler-Smith, C., Zalloua, P. A., and The Genographic Consortium. 2011. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. European Journal of Human Genetics 19: 334–340. Suppl. Info. † Equal contributors
3.	Melé, M., Javed, A., Pybus, M., Calafell, F., Parida, L., Bertranpetit, J., and The Genographic Consortium. 2010. A new method to reconstruct recombination events at a genomic scale. PLoS Computational Biology 6: Article e1001010. Support. Info.		Open Access
2.	Qin, Z., Yang, Y., Kang, L., Yan, S., Cho, K., Cai, X., Lu, Y., Zheng, H., Zhu, D., Fei, D., Li, S., Jin, L., Li, H., and The Genographic Consortium. 2010. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the Last Glacial Maximum. American Journal of Physical Anthropology 143: 555–569. Support. Info.
1.	Haak, W., Balanovsky, O., Sanchez, J. J., Koshel, S., Zaporozhchenko, V., Adler, C. J., Der Sarkissian, C. S. I., Brandt, G., Schwarz, C., Nicklisch, N., Dresely, V., Fritsch, B., Balanovska, E., Villems, R., Meller, H., Alt, K. W., Cooper, A., and The Genographic Consortium. 2010. Ancient DNA from European Early Neolithic farmers reveals their Near Eastern affinities. PLoS Biology 8: Article e1000536. Support. Info.		Open Access

Theses