Behling, A.H., L.D. Shepherd and M.P. Cox. 2020. The importance and prevalence of allopolyploidy in Aotearoa New Zealand. Journal of the Royal Society of New Zealand 50:189-210. PDF
Cagnano, G., I. Lenk, N. Roulund, C.S. Jensen, M.P. Cox and T. Asp. 2020. Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis). Mycologia. In Press.
Denton-Giles, M., H. McCarthy, T. Sehrish, Y. Dijkwel, C.H. Mesarich, R.E. Bradshaw, M.P. Cox and P.P. Dijkwel. 2020. Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae. Molecular Plant Pathology 21:512–526. PDF, Supplemental Materials
Glare, T.R., A. Durrant, C. Berry, L. Palma, M.M. Ormskirk and M.P. Cox. 2020. Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus. Genomics 112:1042-1053. PDF, Supplemental Materials
Inwood, S.N., G. McLaughlin, T.R. Buckley, M.P. Cox, K.M. Handley, T.E. Steeves, T.J. Strabala, R. McDougal and P.K. Dearden. 2020. Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand's bioheritage. New Zealand Journal of Ecology. In Press.
Kondratev, N., M. Denton-Giles, R.E. Bradshaw, M.P. Cox and P.P. Dijkwel. 2020. Camellia plant resistance and susceptibility to petal blight disease are defined by the timing of defence responses. Molecular Plant-Microbe Interactions. In Press.
Kusuma, P., N. Brucato, M.P. Cox, C. Nuraini, T. Letellier, P. Grangé, H. Sudoyo and F.-X. Ricaut. 2020. A genomic perspective of the origin and dispersal of the Bajaw sea nomads in Indonesia. In B. Bellina, R. Blench and J.-C. Gallipaud, Sea Nomads’ Past. National University of Singapore Press: Singapore. In Press.
Natri, H.M., K.S. Bobowik, P. Kusuma, C.C. Darusallam, G.S. Jacobs, G. Hudjashov, J.S. Lansing, Herawati Sudoyo, N.E. Banovich*, M.P. Cox* and I. Gallego Romero*. 2020. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genetics. In Press. *Joint senior authors
Winter, D.J., N.D. Charlton, N. Krom, J. Shiller, C.H. Bock, M.P. Cox and C.A. Young. 2020. Chromosome-level reference genome of Venturia effusa, causative agent of pecan scab. Molecular Plant-Microbe Interactions 33:149-152. PDF, Supplemental Materials
Bradshaw, R.E., S. Ormond, P.-Y. Dupont, P. Chettri, I.K. Ozturk, R.L. McDougal, L.S. Bulman and M.P. Cox. 2019. Reduced virulence of an introduced forest pathogen over 50 years. Microorganisms 7:420. PDF, Supplemental Materials
Bradshaw, R.E., A.D. Sim, P. Chettri, P.-Y. Dupont, Y. Guo, L. Hunziker, R.L. McDougal, A. Van der Nest, A. Fourie, D. Wheeler, M.P. Cox and I. Barnes. 2019. Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains. Molecular Plant Pathology 20:784-799. PDF, Supplemental Materials
Brucato, N., V. Fernandes, P. Kusuma, V. Černý, C.J. Mulligan, P. Soares, T. Rito, C. Besse, A. Boland, J.-F. Deleuze, M.P. Cox, H. Sudoyo, M. Stoneking, L. Pereira and F.-X. Ricaut. 2019. Evidence of Austronesian genetic lineages in East Africa and South Arabia: complex dispersal from Madagascar and Southeast Asia. Genome Biology and Evolution 11:748-758. PDF, Supplemental Materials
Brzozowska, M.M., E. Havula, R.B. Allen and M.P. Cox. 2019. Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians. Reviews in Endocrine and Metabolic Disorders 20:321-332. PDF
Bücking, R., M.P. Cox, G. Hudjashov, L. Saag, H. Sudoyo and M. Stoneking. 2019. Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics 20:1017. PDF, Supplemental Materials
Chujo, T., Y. Lukito, C.J. Eaton, P.-Y. Dupont, L.J. Johnson, D. Winter, M.P. Cox and D.B. Scott. 2019. Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genetics and Biology 125:71–83. PDF, Supplemental Materials
Chung, N.N., G.S. Jacobs, H. Sudoyo, S.G. Malik, L.Y. Chew, J.S. Lansing and M.P. Cox. 2019. Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales. Royal Society Open Science 6:190733. PDF
Cox, M.P. 2019. Calibrating the clock. In D.H. O'Rourke, A Companion to Anthropological Genetics. John Wiley & Sons: New Jersey. pp. 47-56. PDF.
Griffiths, A.G., R. Moraga, M. Tausen, V. Gupta, T.P. Bilton, M.A. Campbell, R. Ashby, I. Nagy, A. Khan, A. Larking, C. Anderson, B. Franzmayr, K. Hancock, A. Scott, N.W. Ellison, M.P. Cox, T. Asp, T. Mailund, M.H. Schierup and S.U. Andersen. 2019. Breaking free: the genomics of allopolyploidy-facilitated niche expansion in White Clover. The Plant Cell 31:1466-1487. PDF, Supplemental Materials, Editorial
Jacobs, G.S., G. Hudjashov, L. Saag, P. Kusuma, C.C. Darusallam, D.J. Lawson, M. Mondal, L. Pagani, F.-X. Ricaut, M. Stoneking, M. Metspalu, H. Sudoyo, J.S. Lansing and M.P. Cox. 2019. Multiple deeply divergent Denisovan ancestries in Papuans. Cell 177:1010-1021. PDF, Supplemental Materials, Cover Image
Lansing, J.S. and M.P. Cox. 2019. Islands of Order: A Guide to Complexity Modeling for the Social Sciences. Princeton Studies in Complexity: Princeton University Press. Order
Moravec, J.C, S. Marsland and M.P. Cox. 2019. Warfare induces post-marital residence change. Journal of Theoretical Biology 474:52-62. PDF, Supplemental Materials
Wall, J.D., A. Ratan, E. Stawiski, H. L. Kim, C. Kim, R. Gupta, K. Suryamohan, E.S. Gusareva, R.W. Purbojati, T. Bhangale, V. Stepanov, V. Kharkov, M.S. Schröder, V. Ramprasad, J. Tom, S. Durinck, Q. Bei, J. Li, J. Guillory, S. Phalke, A. Basu, J. Stinson, S. Nair, S. Malaichamy, N.K. Biswas, J.C. Chambers, K.C. Cheng, J.T. George, S.S. Khor, J.-I. Kim, B. Cho, R. Menon, T. Sattibabu, A. Bassi, M. Deshmukh, A. Verma, V. Gopalan, J.-Y. Shin, M. Pratapneni, S. Santhosh, K. Tokunaga, B.M. Md-Zain, K.G. Chan, M. Parani, P. Natarajan, M. Hauser, R.R. Allingham, C. Santiago-Turla, A. Ghosh, S.G.K. Gadde, C. Fuchsberger, L. Forer, S. Schoenherr, H. Sudoyo, J.S. Lansing, J. Friedlaender, G. Koki, M.P. Cox, M. Hammer, T. Karafet, K.C. Ang, S.Q. Mehdi, V. Radha, V. Mohan, P.P. Majumder, S. Seshagiri, J.-S. Seo, S. Schuster and A.S. Peterson. 2019. Identification of African-specific admixture between modern and archaic humans. American Journal of Human Genetics 105:1254–1261. PDF, Supplemental Materials
Wall, J.D., E. Stawiski, A. Ratan, H. L. Kim, C. Kim, R. Gupta, K. Suryamohan, E.S. Gusareva, R.W. Purbojati, T. Bhangale, V. Stepanov, V. Kharkov, M.S. Schröder, V. Ramprasad, J. Tom, S. Durinck, Q. Bei, J. Li, J. Guillory, S. Phalke, A. Basu, J. Stinson, S. Nair, S. Malaichamy, N.K. Biswas, J.C. Chambers, K.C. Cheng, J.T. George, S.S. Khor, J.-I. Kim, B. Cho, R. Menon, T. Sattibabu, A. Bassi, M. Deshmukh, A. Verma, V. Gopalan, J.-Y. Shin, M. Pratapneni, S. Santhosh, K. Tokunaga, B.M. Md-Zain, K.G. Chan, M. Parani, P. Natarajan, M. Hauser, R.R. Allingham, C. Santiago-Turla, A. Ghosh, S.G.K. Gadde, C. Fuchsberger, L. Forer, S. Schoenherr, H. Sudoyo, J.S. Lansing, J. Friedlaender, G. Koki, M.P. Cox, M. Hammer, T. Karafet, K.C. Ang, S.Q. Mehdi, V. Radha, V. Mohan, P.P. Majumder, S. Seshagiri, J.-S. Seo, S. Schuster and A.S. Peterson. 2019. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576:106-111. PDF, Supplemental Materials, Cover Image
Wu, B. and M.P. Cox. 2019. Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi. Molecular Ecology 28:5103–5114. PDF, Supplemental Materials
Zammit, N.W., O.M. Siggs, P. Gray, K. Horikawa, D.B. Langley, S.N. Walters, S.R. Daley, C. Loetsch, J. Warren, J.Y. Yap, D. Cultrone, A. Russell, E.K. Malle, J.E. Villanueva, M.J. Cowley, V. Gayevskiy, M.E. Dinger, R. Brink, D. Zahra, G. Chaudhri, G. Karupiah, B. Whittle, C. Roots, E. Bertram, M. Yamada, Y. Jeelall, A. Enders, B.E. Clifton, P.D. Mabbitt, C.J. Jackson, S.R. Watson, C.N. Jenne, L.L. Lanier, T. Wiltshire, M.H. Spitzer, G.P. Nolan, F. Schmitz, A. Aderem, B.T. Porebski, A.M. Buckle, D.W. Abbott, J.B. Ziegler, M.E. Craig, P. Benitez-Aguirre, J. Teo, S.G. Tangye, C. King, M. Wong, M.P. Cox, W. Phung, J. Tang, W. Sandoval, I.E. Wertz, D. Christ, C.C. Goodnow and S.T. Grey. 2019. Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Nature Immunology 20:1299-1310. PDF, Supplemental Materials, Cover Image
Bedford, S., R. Blust, D.V. Burley, M.P. Cox, P.V. Kirch, E. Matisoo-Smith, Å. Næss, A. Pawley, C. Sand and P. Sheppard. 2018. Ancient DNA and its contribution to understanding the human history of the Pacific Islands. Archaeology in Oceania 53:205–219. PDF
Brucato, N., V. Fernandes, S. Mazières, P. Kusuma, M.P. Cox, J.W. Ng’ang’a, M. Omar, M.-C. Simeone-Senelle, C. Frassati, F. Alshamali, B. Fin, A. Boland, J.-F. Deleuze, M. Stoneking, A. Adelaar, A. Crowther, N. Boivin, L. Pereira, P. Bailly, J. Chiaroni and F.-X. Ricaut. 2018. The Comoros show the earliest Austronesian gene flow into the Swahili Corridor. American Journal of Human Genetics 10:58-68. PDF, Supplemental Materials, Article Highlighted in Nature
Cox, M.P. 2018. Molecular clock. In W. Trevathan, M. Cartmill, D. Dufour, C. Larsen, D. O’Rourke, K. Rosenberg, K. Strier, The International Encyclopedia of Biological Anthropology, Vol. II. John Wiley & Sons: New Jersey. pp. 1025-1029. PDF
Hudjashov, G., P. Endicott, H. Post, N. Nagle, S.Y.W. Ho, D.J. Lawson, M. Reidla, M. Karmin, S. Rootsi, E. Metspalu, L. Saag, R. Villems, M.P. Cox, R.J. Mitchell, R.L. Garcia-Bertrand, M. Metspalu and R.J. Herrera. 2018. Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Scientific Reports 8:1823. PDF, Supplemental Materials, Article in the Top 10 Genetics and Heredity papers in 2018
Moravec, J.C., Q. Atkinson, C. Bowern, S.J. Greenhill, F.M. Jordan, R.M. Ross, R. Gray, S. Marsland and M.P. Cox. 2018. Post-marital residence patterns show lineage-specific evolution. Evolution and Human Behavior 39:594-601. PDF, Supplemental Materials
Robertson, S.P., J.H. Hindmarsh, S. Berry, V.A. Cameron, M.P. Cox, O. Dewes, R.N. Doughty, G. Gray, J.C. Jacobsen, A. Laurence, E. Matisoo-Smith, S. Morton, A.N. Shelling, D. Sika-Paotonu, A. Rolleston, J.R. Skinner, R.G. Snell, A. Sporle, C. Print, T.R. Merriman, M. Hudson and P. Wilcox. 2018. Genomic medicine must reduce, not compound, health inequities: the case for hauora-enhancing genomic resources for New Zealand. New Zealand Medical Journal 131:81-89. PDF, Editorial
Wehi, P.M., M.P. Cox, T. Roa and H. Whaanga. 2018. Human perceptions of megafaunal extinction events revealed by linguistic analysis of indigenous oral traditions. Human Ecology 46:461-470. PDF, Supplemental Materials
Whaanga, H., P. Wehi, M.P. Cox, T. Roa and I. Kusabs. 2018. Māori oral traditions record and convey indigenous knowledge of marine and freshwater resources. New Zealand Journal of Marine and Freshwater Research 52:487-496. PDF
Winter, D.J., A.R.D. Ganley, C.A. Young, I. Liachko, C.L. Schardl, P.-Y. Dupont, D. Berry, A. Ram, B. Scott and M.P. Cox. 2018. Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genetics 14:e1007467. PDF, Supplemental Materials
Brucato, N., P. Kusuma, P. Beaujard, H. Sudoyo, M.P. Cox and F.-X. Ricaut. 2017. Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Scientific Reports 7:2919. PDF, Supplemental Materials
Burgess, S.A., S.H. Flint, D. Lindsay, M.P. Cox and P.J. Biggs. 2017. Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiology 17:140. PDF, Supplemental Materials
Campbell, M.A., B.A. Tapper, W.R. Simpson, R.D. Johnson, W. Mace, A. Ram, Y. Lukito, P.-Y. Dupont, L.J. Johnson, D.B. Scott, A.R.D. Ganley, and M.P. Cox. 2017. Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy. Mycologia 109:715-729. PDF, Supplemental Materials
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: Prehistory and Human Migration in Island Southeast Asia, Chapter 4. John Wiley & Sons: New Jersey. pp. 107-116. PDF
Dupont, P.-Y. and M.P. Cox. 2017. Genomic data quality impacts automated detection of lateral gene transfer in fungi. G3: Genes | Genomes | Genetics 7:1301-1314. PDF, Supplemental Materials
Hudjashov, G., T.M. Karafet, D. Lawson, S. Downey, O. Savina, H. Sudoyo, J.S. Lansing, M.F. Hammer and M.P. Cox. 2017. Complex patterns of admixture across the Indonesian Archipelago. Molecular Biology and Evolution 34:2439-2452. PDF, Supplemental Materials, Article Highlighted by the Editor ('Fast Track')
Kusuma, P., N. Brucato, M.P. Cox, T. Letellier, A. Manan, C. Nuraini, P. Grangé, H. Sudoyo and F.-X. Ricaut. 2017. The last sea nomads of the Indonesian archipelago: genomic origins and dispersal. European Journal of Human Genetics 25:1004-1010. PDF, Supplemental Materials
Lansing, J.S., C. Abundo, G.S. Jacobs, E.G. Guillot, S. Thurner, S.S. Downey, L.Y. Chew, T. Bhattacharya, N.N. Chung, H. Sudoyo and M.P. Cox. 2017. Kinship structures create persistent channels for language transmission. Proceedings of the National Academy of Sciences USA 114:12910-12915. PDF, Supplemental Materials
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
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, Runner up for Science's 'Breakthrough of the Year' paper
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
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, Code
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, Data, 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, Code, Article Highlighted by the Editor
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, Code
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, Code, Data
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, Data
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, Code
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, Code, Data
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
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, Code, 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, Code
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
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, Code, 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, Code, 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, Data, Code, 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, Code
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
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, Code (TMRCA), Code (ρ), 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, Code, 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, Data (mtDNA), Data (Y chromosome)
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
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, Code
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, Code
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
