Publications

2017

Cox, M.P. 2017. The Genetic History of Human Populations in Island Southeast Asia during the Late Pleistocene and Holocene. In P. Bellwood, First Islanders: The Prehistory of Island Southeast Asia. John Wiley & Sons: New Jersey. In Press.

Cox, M.P. 2017. Calibrating the Clock. In D.H. O'Rourke, A Companion to Anthropological Genetics. John Wiley & Sons: New Jersey. In Press.

Cox, M.P. 2017. Molecular Clocks. In W. Trevathan, The International Encyclopedia of Biological Anthropology. John Wiley & Sons: New Jersey. In Press.

Dupont, P.-Y. and M.P. Cox. 2017. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3. In Press.

Schmid, J., R. Day, N. Zhang, P.-Y. Dupont, M.P. Cox, C.L. Schardl, N. Minards, M. Truglio, N. Moore, D.R. Harris and Y. Zhou. 2017. Host Tissue Environment Directs Activities of an Epichloë Endophyte, while it Induces Systemic Hormone and Defense Responses in its Native Perennial Ryegrass Host. Molecular Plant-Microbe Interactions 30:138-149. PDF, Supplemental Materials

2016

Bradshaw, R.E., Y. Guo, A.D. Sim, M.S. Kabir, P. Chettri, I.K. Ozturk, L. Hunziker, R.J. Ganley and M.P. Cox. 2016. Genome-Wide Gene Expression Dynamics of the Fungal Pathogen Dothistroma septosporum throughout its Infection Cycle of the Gymnosperm Host Pinus radiata. Molecular Plant Pathology 17:210-224. PDF, Supplemental Materials

Brucato, N., P. Kusuma, M.P. Cox, D. Pierron, G.A. Purnomo, A. Adelaar, T. Kivisild, T. Letellier, H. Sudoyo and F.-X. Ricaut. 2016. Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo. Molecular Biology and Evolution 33:2396–2400. PDF, Supplemental Materials

Campbell, M.A., A.R.D. Ganley, T. Gabaldón and M.P. Cox. 2016. The Case of the Missing Ancient Fungal Polyploids. The American Naturalist 188:602-614. PDF, Supplemental Materials

Cox, M.P.*, G. Hudjashov*, A. Sim, O. Savina, T.M. Karafet, H. Sudoyo and J.S. Lansing. 2016. Small Traditional Human Communities Sustain Genomic Diversity Over Microgeographic Scales Despite Linguistic Isolation. Molecular Biology and Evolution 33:2273–2284. *Joint first authors. PDF, Supplemental Materials

Guillot, E.G. and M.P. Cox. 2016. High Frequency Haplotypes are Expected Events, not Historical Figures. F1000 Research 4:666. PDF

Hazelton, M.L. and M.P. Cox. 2016. Bandwidth Selection for Kernel Log-Density Estimation. Computational Statistics and Data Analysis 103:56-67. PDF

Kusuma, P., N. Brucato, M.P. Cox, D. Pierron, H. Razafindrazaka, A. Adelaar, H. Sudoyo, T. Letellier and F.-X. Ricaut. 2016. Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy. Scientific Reports 6:26066. PDF, Supplemental Materials

Kusuma, P., M.P. Cox, N. Brucato, H. Sudoyo, T. Letellier and F.-X. Ricaut. 2016. Western Eurasian Genetic Influences in the Indonesian Archipelago. Quaternary International 416:243-248. PDF, Supplemental Materials

Lange, C., R.J. Weld, M.P. Cox, R.E. Bradshaw, K.L. McLean, A. Stewart and J.M. Steyaert. 2016. Genome-Scale Investigation of Phenotypically Distinct But Nearly Clonal Trichoderma Strains. PeerJ 4:e2023. PDF, Supplemental Materials

Mellow, K., P. Chettri, S. Kabir, R.L. McDougal, M.P. Cox, A. Stewart, C. Lange, J.M. Steyaert and R.E. Bradshaw. 2016. Molecular Markers for Quantification of Bioactive Fungal Strains Associated with Pinus radiata. New Zealand Plant Protection 69:64-67. PDF

Pagani, L., D.J. Lawson, E. Jagoda, A. Mörseburg, A. Eriksson, M. Mitt, F. Clemente, G. Hudjashov, M. DeGiorgio, L. Saag, J.D. Wall, A. Cardona, R. Mägi, M.A. Wilson Sayres, S. Kaewert, C. Inchley, C.L. Scheib, M. Järve, M. Karmin, G.S. Jacobs, T. Antao, F.M. Iliescu, A. Kushniarevich, Q. Ayub, C. Tyler-Smith, Y. Xue, B. Yunusbayev, K. Tambets, C.B. Mallick, L. Saag, E. Pocheshkhova, G. Andriadze, C. Muller, M.C. Westaway, D.M. Lambert, G. Zoraqi, S. Turdikulova, D. Dalimova, Z. Sabitov, G.N.N. Sultana, J. Lachance, S. Tishkoff, K. Momynaliev, J. Isakova, L.D. Damba, M. Gubina, P. Nymadawa, I. Evseeva, L. Atramentova, O. Utevska, F.-X. Ricaut, N. Brucato, H. Sudoyo, T. Letellier, M.P. Cox, N.A. Barashkov, V. Škaro, L. Mulahasanović, D. Primorac, H. Sahakyan, M. Mormina, C.A. Eichstaedt, D.V. Lichman, S. Abdullah, G. Chaubey, J.T.S. Wee, E. Mihailov, A. Karunas, S. Litvinov, R. Khusainova, N. Ekomasova, V. Akhmetova, I. Khidiyatova, D. Marjanović, L. Yepiskoposyan, D.M. Behar, E. Balanovska, A. Metspalu, M. Derenko, B. Malyarchuk, M. Voevoda, S.A. Fedorova, L.P. Osipova, M.M. Lahr, P. Gerbault, M. Leavesley, A.B. Migliano, M. Petraglia, O. Balanovsky, E.K. Khusnutdinova, E. Metspalu, M.G. Thomas, A. Manica, R. Nielsen, R. Villems, E. Willerslev, T. Kivisild and M. Metspalu. 2016. Genomic Analyses Inform on Migration Events During the Peopling of Eurasia. Nature 538:238-242. PDF, Supplemental Materials, Cover Image

Skoglund, P., C. Posth, K. Sirak, M. Spriggs, F. Valentin, S. Bedford, G.R. Clark, C. Reepmeyer, F. Petchey, D. Fernandes, Q. Fu, E. Harney, M. Lipson, S. Mallick, M. Novak, N. Rohland, K. Stewardson, S. Abdullah, M.P. Cox, F.R. Friedlaender, J.S. Friedlaender, T. Kivisild, G. Koki, P. Kusuma, D.A. Merriwether, F.-X. Ricaut, J.T.S. Wee, N. Patterson, J. Krause, R. Pinhasi and D. Reich. 2016. Genomic Insights into the Peopling of the Southwest Pacific. Nature 538:510-513. PDF, Supplemental Materials

Vallée, F., A. Luciani and M.P. Cox. 2016. Reconstructing Demography and Social Behavior during the Neolithic Expansion from Genomic Diversity across Island Southeast Asia. Genetics 204:1495–1506. PDF, Supplemental Materials, Supplemental Movie, Article Highlighted by the Editor

2015

Amaris, A.J.R. and M.P. Cox. 2015. A Flexible Theoretical Representation for the Temporal Dynamics of Structured Populations as Paths on Polytope Complexes. Journal of Mathematical Biology 71:735-766. PDF

Berry, D., M.P. Cox and B. Scott. 2015. Draft Genome Sequence of the Filamentous Fungus Penicillium paxilli (ATCC 26601). Genome Announcements 3:e00071-15. PDF

Burgess, S.A., M.P. Cox, S.H. Flint, D. Lindsay and P.J. Biggs. 2015. Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant. Genome Announcements 3:e00939-15. PDF

Duchemin, W., P.-Y. Dupont, M.A. Campbell, A.R.D. Ganley and M.P. Cox. 2015. HyLiTE: Accurate and Flexible Analysis of Gene Expression in Hybrid and Allopolyploid Species. BMC Bioinformatics 16:8. PDF, Supplemental Materials

Dupont, P.-Y., C.J. Eaton, J.J. Wargent, S. Fechtner, P. Solomon, J. Schmid, R.C. Day, D.B. Scott and M.P. Cox. 2015. Fungal Endophyte Infection of Ryegrass Reprograms Host Metabolism and Alters Development. New Phytologist 208:1227-1240. PDF, Supplemental Materials, Cover Image

Eaton, C.J., P.-Y. Dupont, P. Solomon, W. Clayton, B. Scott and M.P. Cox. 2015. A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp. Molecular Plant-Microbe Interactions 28:218-231. PDF, Supplemental Materials

Guillot, E.G., M.L. Hazelton, T.M. Karafet, J.S. Lansing, H. Sudoyo and M.P. Cox. 2015. Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity. Molecular Biology and Evolution 32:2254-2262. PDF, Supplemental Materials, SNP Data (300 Mb), MBE Commentary

Karmin, M., L. Saag, M. Vicente, M.A.W. Sayres, M. Järve, U.G. Talas, S. Rootsi, A.-M. Ilumäe, R. Mägi, M. Mitt, L. Pagani, T. Puurand, Z. Faltyskova, F. Clemente, A. Cardona, E. Metspalu, H. Sahakyan, B. Yunusbayev, G. Hudjashov, M. DeGiorgio, E.-L. Loogväli, C. Eichstaedt, M. Eelmets, G. Chaubey, K. Tambets, S. Litvinov, M. Mormina, Y. Xue, Q. Ayub, G. Zoraqi, T.S. Korneliussen, F. Akhatova, J. Lachance, S. Tishkoff, K. Momynaliev, F.-X. Ricaut, P. Kusuma, H. Razafindrazaka, D. Pierron, M.P. Cox, G.N.N. Sultana, R. Willerslev, C. Muller, M. Westaway, D. Lambert, V. Skaro, L. Kovačević, S. Turdikulova, D. Dalimova, R. Khusainova, N. Trofimova, V. Akhmetova, I. Khidiyatova, D.V. Lichman, J. Isakova, E. Pocheshkhova, Z. Sabitov, N.A. Barashkov, P. Nymadawa, E. Mihailov, J.W.T. Seng, I. Evseeva, A.B. Migliano, S. Abdullah, G. Andriadze, D. Primorac, L. Atramentova, O. Utevska, L. Yepiskoposyan, D. Marjanović, A. Kushniarevich, D.M. Behar, C. Gilissen, L. Vissers, J. Veltman, E. Balanovska, M. Derenko, B. Malyarchuk, A. Metspalu, S. Fedorova, A. Eriksson, A. Manica, F. Mendez, T.M. Karafet, K. Veeramah, N. Bradman, M.F. Hammer, L.P. Osipova, O. Balanovsky, E.K. Khusnutdinova, K. Johnsen, M. Remm, M.G. Thomas, C. Tyler-Smith, P.A. Underhill, E. Willerslev, R. Nielsen, M. Metspalu, R. Villems and T. Kivisild. 2015. A Recent Bottleneck of Y Chromosome Diversity Coincides with a Global Change in Culture. Genome Research 25:459-466. PDF, Supplemental Materials

Kusuma, P., M.P. Cox, D. Pierron, H. Razafindrazaka, N. Brucato, L. Tonasso, H.L. Suryadi, T. Letellier, H. Sudoyo and F.-X. Ricaut. 2015. Mitochondrial DNA and the Y Chromosome Suggest the Settlement of Madagascar by Indonesian Sea Nomad Populations. BMC Genomics 16:191. PDF, Supplemental Materials, Designated a ‘Highly Accessed’ article by BioMed Central

Nicholson, M.J., C.J. Eaton, C. Stärkel, B.A. Tapper, M.P. Cox and B. Scott. 2015. Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum. Toxins 7:2701-2722. PDF

Sanderson, J., H. Sudoyo, T.M. Karafet, M.F. Hammer and M.P. Cox. 2015. Reconstructing Past Admixture Processes from Local Genomic Ancestry using Wavelet Transformation. Genetics 200:469-481. PDF, Supplemental Materials, Article Highlighted by the Editor

2014

Cox, M.P., T. Dong, G. Shen, Y. Dalvi, D.B. Scott and A.R.D. Ganley. 2014. An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns. PLoS Genetics 10:e1004180. PDF, Supplemental Materials

Guillot, E.G. and M.P. Cox. 2014. SMARTPOP: Inferring the Impact of Social Dynamics on Genetic Diversity through High Speed Simulations. BMC Bioinformatics 15:175. PDF, Supplemental Materials

Lansing, J.S., S.A. Cheong, L.Y. Chew, M.P. Cox, M.-H.R. Ho and W.A. Arthawiguna. 2014. Regime Shifts in Balinese Subaks. Current Anthropology 55:232-239. PDF, Supplemental Materials

Prangle, D., P. Fearnhead, M.P. Cox, P.J. Biggs and N.P. French. 2014. Semi-Automatic Selection of Summary Statistics for ABC Model Choice. Statistical Applications in Genetics and Molecular Biology 13:67-82. PDF, Supplemental Materials

Schardl, C.L., C.A. Young, N. Moore, N. Krom, P.-Y. Dupont, J. Pan, S. Florea, J.S. Webb, J. Jaromczyk, J.W. Jaromczyk, M.P. Cox and M.L. Farman. 2014. Genomes of Plant-Associated Clavicipitaceae. Advances in Botanical Research 70:291-327. PDF

Tumonggor, M.K., T.M. Karafet, S. Downey, J.S. Lansing, P. Norquest, H. Sudoyo, M. Hammer and M.P. Cox. 2014. Isolation, Contact and Social Behavior Shaped Genetic Diversity in West Timor. Journal of Human Genetics 59:494–503. PDF, Supplemental Materials, Supplemental Dataset

2013

Bradshaw, R.E., J.C. Slot, G.G. Moore, P. Chettri, P.J.G.M. de Wit, K.C. Ehrlich, A.R.D. Ganley, M.A. Olson, A. Rokas, I. Carbone and M.P. Cox. 2013. Fragmentation of an Aflatoxin-Like Gene Cluster in a Forest Pathogen. New Phytologist 198:525-535. PDF, Supplemental Materials

Chettri, P., K.C. Ehrlich, J.W. Cary, J. Collemare, M.P. Cox, S.A. Griffiths, M.A. Olson, P.J.G.M. de Wit and R.E. Bradshaw. 2013. Dothistromin Genes at Multiple Separate Loci are Regulated by AflR. Fungal Genetics and Biology 51:12-20. PDF, Supplemental Materials, Supplemental Dataset

Cox, M.P. 2013. Southeast Asia Islands and Oceania: Human Genetics. In I. Ness and P. Bellwood (eds.), Encyclopedia of Global Human Migration, Volume 1, Prehistory, Chapter 37. Wiley-Blackwell: Indianapolis, USA. pp. 293-301. PDF

Cox, M.P., B.R. Holland, M.C. Wilkins and J. Schmid. 2013. Reconstructing Past Changes in Locus-Specific Recombination Rates. BMC Genetics 14:11. PDF, Supplemental Materials

Guillot, E.G., M.K. Tumonggor, J.S. Lansing, H. Sudoyo and M.P. Cox. 2013. Climate Change Influenced Female Population Sizes through Time across the Indonesian Archipelago. Human Biology 85:135-152. PDF

Schardl, C.L., C.A. Young, U. Hesse, S.G. Amyotte, K. Andreeva, P.J. Calie, D.J. Fleetwood, D.C. Haws, N. Moore, B. Oeser, D.G. Panaccione, K.K. Schweri, C.R. Voisey, M.L. Farman, J.W. Jaromczyk, B.A. Roe, D.M. O'Sullivan, B. Scott, P. Tudzynski, Z. An, E.G. Arnaoudova, C.T. Bullock, N.D. Charlton, L. Chen, M.P. Cox, R.D. Dinkins, S. Florea, A.E. Glenn, A. Gordon, U. Güldener, D.R. Harris, W. Hollin, J. Jaromczyk, R.D. Johnson, A.K. Khan, E. Leistner, A. Leuchtmann, C. Li, J.-G. Liu, J. Liu, M. Liu, W. Mace, C. Machado, P. Nagabhyru, J. Pan, J. Schmid, K. Sugawara, U. Steiner, J.E. Takach, E. Tanaka, J.S. Webb, E.V. Wilson, J. Wiseman, R. Yoshida and Z. Zeng. 2013. Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genetics 9:e1003323. PDF, Supplemental Materials

Tumonggor, M.K., T.M. Karafet, B. Hallmark, J.S. Lansing, H. Sudoyo, M.F. Hammer and M.P. Cox. 2013. The Indonesian Archipelago: An Ancient Genetic Highway Linking Asia and the Pacific. Journal of Human Genetics 58:165-173. PDF, Supplemental Materials, Supplemental Dataset

Wehi, P., M.P. Cox, T. Roa and H. Whaanga. 2013. Marine Resources in Māori Oral Tradition: He Kai Moana, he Kai mā te Hinengaro. Journal of Marine and Island Cultures 2:59–68. PDF

2012

Cox, M.P., M.G. Nelson, M.K. Tumonggor, F.-X. Ricaut and H. Sudoyo. 2012. A Small Cohort of Island Southeast Asian Women Founded Madagascar. Proceedings of the Royal Society B 279:2761-2768. PDF, BBC World Interview

de Wit, P.J.G.M., A. van der Burgt, B. Ökmen, I. Stergiopoulos, A.L. Aerts, A.H.A. Bahkali, H. Beenen, P. Chettri, M.P. Cox, E. Datema, R.P. de Vries, B. Dhillon, A.R. Ganley, Y. Guo, R.C. Hamelin, B. Henrissat, M.S. Kabir, M.K. Jashni, G. Kema, S. Klaubauf, A. Lapidus, A. Levasseur, E. Lindquist, S. Lucas, R. Mehrabi, R.A. Ohm, T.J. Owen, A. Salamov, A. Schwelm, E. Schijlen, H. Sun, H.A. van den Burg, R.C.H.J. van Ham, S. Zhang, S.B. Goodwin, I.V. Grigoriev, J. Collemare and R.E. Bradshaw. 2012. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles but also Signatures of Common Ancestry. PLoS Genetics 8:e1003088. PDF, Supplemental Materials

Eaton, C.J., I.E. Cabrera, J.A. Servin, S.J. Wright, M.P. Cox and K.A. Borkovich. 2012. The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in Neurospora crassa. PLoS ONE 7:e48026. PDF

Ricaut, F.-X.*, M.P. Cox*, M. Lacan, C. Keyser, F. Duranthon, B. Ludes, J. Guilaine and E. Crubézy. 2012. A Time Series of Prehistoric Mitochondrial DNA Reveals Western European Genetic Diversity was largely Established by the Bronze Age. Advances in Anthropology 2:14-23. *Joint first authors. PDF, Supplemental Movie

2011

Eaton, C.J., M.P. Cox and D.B. Scott. 2011. What Triggers Grass Endophytes to Switch from Mutualism to Pathogenism? Plant Science 180:190-195. PDF

Lansing, J.S. and M.P. Cox. 2011. The Domain of the Replicators: Selection, Neutrality and Cultural Evolution. Current Anthropology 52:105-125. PDF

Lansing, J.S., M.P. Cox, T.A. de Vet, S.S. Downey, B. Hallmark and H. Sudoyo. 2011. An Ongoing Austronesian Expansion in Island Southeast Asia. Journal of Anthropological Archaeology 30:262-272. PDF

Russell, A.L.*, M.P. Cox*, V.A. Brown and G.F. McCracken. 2011. Population Growth of Mexican Free-Tailed Bats (Tadarida brasiliensis mexicana) Predates Human Agricultural Activity. BMC Evolutionary Biology 11:88. *Joint first authors. PDF, Supplemental Materials

Wilder, J.A., M.P. Cox, A.M. Paquette, R. Alford, A.W. Satyagraha, A. Harahap and H. Sudoyo. 2011. Genetic Continuity across a Deeply Divergent Linguistic Contact Zone in North Maluku, Indonesia. BMC Genetics 12:100. PDF, Editor’s Pick 2012

2010

Cox, M.P., C.J. Eaton and D.B. Scott. 2010. Exploring Molecular Signaling in Plant-Fungal Symbioses using High Throughput RNA Sequencing. Plant Signaling and Behavior 5:1353-1358. PDF

Cox, M.P., and M.F. Hammer. 2010. A Question of Scale: Human Migrations Writ Large and Small. BMC Biology 8:98. PDF, Designated a ‘Highly Accessed’ article by BioMed Central

Cox, M.P., T.M. Karafet, J.S. Lansing, H. Sudoyo and M.F. Hammer. 2010. Autosomal and X-Linked Single Nucleotide Polymorphisms Reveal a Steep Asian-Melanesian Ancestry Cline in Eastern Indonesia and a Sex Bias in Admixture Rates. Proceedings of the Royal Society B 277:1589-1596. PDF, Supplemental Materials, Data

Cox, M.P., and J.S. Lansing. 2010. Reply to “Farming and Language in Island Southeast Asia: Reframing Austronesian History”. Current Anthropology 51:241-242. PDF, Invited response to Donohue, M. and T. Denham. 2010. Current Anthropology 51:223-256

Cox, M.P., D.A. Peterson and P.J. Biggs. 2010. SolexaQA: At-a-Glance Quality Assessment of Illumina Second-Generation Sequencing Data. BMC Bioinformatics 11:485. PDF, Designated a ‘Highly Accessed’ article by BioMed Central

Eaton, C.J., M.P. Cox, B. Ambrose, M. Becker, U. Hesse, C.L. Schardl and D.B. Scott. 2010. Disruption of Signaling in a Fungal-Grass Symbiosis Leads to Pathogenesis. Plant Physiology 153:1780-1794. PDF, Supplemental Materials 1, Supplemental Materials 2, Supplemental Materials 3, Supplemental Materials 4, Press Release, Media Coverage

Hammer, M.F., A.E. Woerner, F.L. Mendez, J.C. Watkins, M.P. Cox and J.D. Wall. 2010. The Ratio of Human X Chromosome to Autosome Diversity is Positively Correlated with Genetic Distance from Genes. Nature Genetics 42:830-831. PDF, Supplemental Materials

Karafet, T.M., B. Hallmark, M.P. Cox, H. Sudoyo, S. Downey, J.S. Lansing and M.F. Hammer. 2010. Major East-West Division Underlies Y Chromosome Stratification Across Indonesia. Molecular Biology and Evolution 27:1833-1844. PDF, Supplemental Materials

Razafindrazaka, H., F.-X. Ricaut, M.P. Cox, M. Mormina, J.-M. Dugoujon, L.P. Randriamarolaza, E. Guitard, L. Tonasso, B. Ludes and E. Crubézy. 2010. Complete Mitochondrial DNA Sequences Provide New Insights into the Polynesian Motif and the Peopling of Madagascar. European Journal of Human Genetics 18:575-581. PDF, Supplemental Materials

Ricaut, F.-X., T. Thomas, M. Mormina, M.P. Cox, M. Bellatti, R. Foley and M. Mirazón Lahr. 2010. Ancient Solomon Islands MtDNA: Assessing Holocene Settlement and the Impact of European Contact. Journal of Archaeological Science 37:1161-1170. PDF, Supplemental Materials

2009

Cox, M.P., D.A. Morales, A.E. Woerner, J. Sozanski, J.D. Wall and M.F. Hammer. 2009. Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations. PLoS ONE 4:e6366. PDF, Supplemental Materials

Lansing, J.S., M.P. Cox, S.S. Downey, M.A. Janssen and J.W. Schoenfelder. 2009. A Robust Budding Model of Balinese Water Temple Networks. World Archaeology 41:112-133. PDF

Ricaut, F.-X., H. Razafindrazaka, M.P. Cox, J.-M. Dugoujon, E. Guitard, C. Sambo, M. Mormina, M. Mirazón Lahr, B. Ludes and E. Crubézy. 2009. A New Deep Branch of Eurasian MtDNA Macrohaplogroup M Reveals Additional Complexity Regarding the Settlement of Madagascar. BMC Genomics 10:605. PDF, Supplemental Materials 1, Supplemental Materials 2, Supplemental Materials 3

2008

Cox, M.P. 2008. Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations under a Range of Demographic Models. Human Biology 80:335-357. PDF, Selected as the Open Access Article for August 2008 by the editorial board of Human Biology; Gabriel Ward Lasker Prize for best publication in Human Biology in 2008

Cox, M.P. 2008. The Genetic Environment of Melanesia: Clines, Clusters and Contact. In V.T. Koven (ed.), Population Genetics Research Progress, Chapter 2. Nova Science Publishers: New York. pp. 45-83. PDF

Cox, M.P., F.L. Mendez, T.M. Karafet, M. Metni Pilkington, S.B. Kingan, G. Destro-Bisol, B.I. Strassmann and M.F. Hammer. 2008. Testing for Archaic Hominin Admixture on the X-Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region from Summaries of Genealogical Topology under the Structured Coalescent. Genetics 178:427-437. PDF, Supplemental Materials, Media Coverage

Cox, M.P., A.E. Woerner, J.D. Wall and M.F. Hammer. 2008. Intergenic DNA Sequences from the Human X Chromosome Reveal High Rates of Global Gene Flow. BMC Genetics 9:e76. PDF, Supplemental Materials, Designated a ‘Highly Accessed’ article by BioMed Central

Downey, S.S., B. Hallmark, M.P. Cox, P. Norquest and J.S. Lansing. 2008. Computational Feature-Sensitive Reconstruction of Language Relationships: Developing the ALINE Distance for Comparative Historical Linguistic Reconstruction. Journal of Quantitative Linguistics 15:340-369. PDF

Hagelberg, E., M.P. Cox, W. Schiefenhövel and I. Frame. 2008. A Genetic Perspective on the Origins and Dispersal of the Austronesians: Mitochondrial DNA Variation from Madagascar to Easter Island. In A. Sanchez-Mazas, R. Blench, M.D. Ross, I. Peiros and M. Lin (eds.), Past Human Migrations in East Asia: Matching Archaeology, Linguistics and Genetics, Chapter 16. Routledge: London. pp. 356-375. PDF

Hammer, M.F., F.L. Mendez, M.P. Cox, A.E. Woerner and J.D. Wall. 2008. Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity. PLoS Genetics 4:e1000202. PDF, Supplemental Materials, Media Coverage

Lansing, J.S., J.C. Watkins, B. Hallmark, M.P. Cox, T.M. Karafet, H. Sudoyo and M.F. Hammer. 2008. Male Dominance Rarely Skews the Frequency Distribution of Y Chromosome Haplotypes in Human Populations. Proceedings of the National Academy of Sciences USA 105:11645-11650. PDF, Supplemental Materials, Media Coverage

Metni Pilkington, M., J.A. Wilder, F.L. Mendez, M.P. Cox, A. Woerner, T. Angui, S. Kingan, Z. Mobasher, C. Batini, G. Destro-Bisol, H. Soodyall, B.I. Strassmann and M.F. Hammer. 2008. Contrasting Signatures of Population Growth for Mitochondrial DNA and Y Chromosomes among Human Populations in Africa. Molecular Biology and Evolution 25:517-525. PDF, mtDNA data, NRY data

Russell, A.L., S.M. Goodman and M.P. Cox. 2008. Coalescent Analyses Support Multiple Mainland-to-Island Dispersals in the Evolution of Malagasy Triaenops Bats (Chiroptera: Hipposideridae). Journal of Biogeography 35:995-1003. PDF

Wall, J.D., M.P. Cox, F.L. Mendez, A. Woerner, T. Severson and M.F. Hammer. 2008. A Novel DNA Sequence Database for Analyzing Human Demographic History. Genome Research 18:1354-1361. PDF, Supplemental Materials, Media Coverage

2007

Cox, M.P., A.J. Redd, T.M. Karafet, C.A. Ponder, J.S. Lansing, H. Sudoyo and M.F. Hammer. 2007. A Polynesian Motif on the Y Chromosome: Population Structure in Remote Oceania. Human Biology 79:525-535. PDF

Garrigan, D., S.B. Kingan, M. Metni Pilkington, J.A. Wilder, M.P. Cox, H. Soodyall, B. Strassmann, G. Destro-Bisol, P. de Knijff, A. Novelletto, J. Friedlaender and M.F. Hammer. 2007. Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow from Mitochondrial, X and Y Chromosome Resequencing Data. Genetics 177:2195-2207. PDF, Supplemental Figures, Supplemental Tables

Lansing, J.S., M.P. Cox, S.S. Downey, B.M. Gabler, B. Hallmark, T.M. Karafet, P. Norquest, J.W. Schoenfelder, H. Sudoyo, J.C. Watkins and M.F. Hammer. 2007. Coevolution of Languages and Genes on the Island of Sumba, Eastern Indonesia. Proceedings of the National Academy of Sciences USA 104:16022-16026. PDF, Letter, Reply

Woerner, A.E., M.P. Cox and M.F. Hammer. 2007. Recombination-Filtered Genomic Datasets by Information Maximization. Bioinformatics 23:1851-1853. PDF

2006

Cox, M.P. 2006. Extreme Patterns of Variance in Small Populations: Placing Limits on Human Y-Chromosome Diversity through Time in the Vanuatu Archipelago. Annals of Human Genetics 71:390-406. PDF

Cox, M.P. 2006. Minimal Hierarchical Analysis of Global Human Y-Chromosome SNP Diversity by PCR-RFLP. Anthropological Science 114:69-74. PDF

Cox, M.P., and M. Mirazón Lahr. 2006. Y-Chromosome Diversity Is Inversely Associated with Language Affiliation in Paired Austronesian- and Papuan-Speaking Communities from Solomon Islands. American Journal of Human Biology 18:35-50. PDF

2005

Cox, M.P. 2005. Indonesian Mitochondrial DNA and Its Opposition to a Pleistocene Era Origin of Proto-Polynesians in Island Southeast Asia. Human Biology 77:179-188. PDF