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Publications (Pubmed list , Google scholar )

  1. Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao, Muhua Wang, Julie Jacquemin, Claude Becker, Dave Kudrna, Jianwei Zhang, Carlos E.M. Londoño, Xiang Song, Seunghee Lee, Paul Sanchez, Andrea Zuccolo, Jetty Amiraju, Jayson Talag, Ann Danowitz, Luis F. Rivera, Andrea R. Gschwend, Christos Noutsos, Cheng-chieh Wu, Shu-min Kao, Jhih-wun Zeng, Fu-jin Wei, Qiang Zhao, Qi Feng, Moaine Elbaidouri, Marie-Christine Carpentier, Eric Lasserre, Richard Cooke, Daniel da Rosa Farias, Luciano Carlos da Maia, Railson S. dos Santos, Kevin G. Nyberg, Chuanzhu Fan, Detlef Weigel, Kshirod K. Jena, Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware, & Rod A. Wing. Genomes of 11 rice relatives unveil genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics (in press)

  2. López-Olmos K., Markow T. A., Machado C. A. (2017) Evolution of GSTD1 in cactophilic Drosophila. J. Mol. Evol. 84: 285-294 ""

  3. Sanchez-Flores A., Penaloza F., Carpinteyro J., Nazario N., Abreu-Goodger C., Machado C. A., Markow T. A. (2016) Genome evolution in three species of cactophilic Drosophila. G3:Genes, Genomes, Genetics 6: 3097-3105""

  4. Nyberg K. G., Machado C. A. (2016) Comparative expression dynamics of long intergenic noncoding RNAs (lincRNAs) in the genus Drosophila. Genome Biol. Evol. 8: 1839-1858 ""
  5. Tian E., Nason J., Machado C. A., Zheng L., Yu H., Kjellberg F. (2015) Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism. Mol. Ecol. 24: 5976–5991 ""

  6. Martinson E. O., Hackett J. D., Machado C. A., Arnold A. E. (2015) Metatranscriptome analysis of fig flowers provides insights into potential mechanisms for mutualism stability and gall induction PLoS One 10(6): e0130745 ""

  7. Flores-Lopez C. A, Machado C. A. (2015) Differences in inferred genome-wide signals of positive selection during the evolution of Trypanosoma cruzi and Leishmania spp. lineages: a result of disparities in host and tissue infection ranges? Infect. Genet. Evol. 33: 37-46 ""
  8. Yang L-Y, Machado C. A., Dang X-D, Peng Y-Q, Yang D-R, Liao W-J, Zhang D-Y. (2015) The incidence and pattern of co-pollinator diversification in dioecious and monoecious figs Evolution 69: 294–304 ""

  9. Wang M., Yu Y., Haberer G., Marri P. R., Fan C., Goicoechea J. L., Zuccolo A., Song X., Kudrna D., Jetty S. S. A., Cossu R. M., Maldonado C., Chen J., Lee S., Sisneros N., Baynast K., Golser W., Wissotski M., Kim W., Sanchez P., Ndjiondjop M-N., Sanni K., Long M., Carney J., Panaud O., Wicker T., Machado C. A., Chen M., Mayer K. F. X., Rounsley S., Wing R.A. (2014) The genome of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics 46: 982-988 ""

  10. Martinson E. O., Jander K. C., Peng Y-Q, Chen H-H, Machado C. A., Arnold A. E., Herre E. A. (2014) Relative investment in egg load and poison sac in fig wasps: implications for physiological mechanisms underlying seed and wasp production in figs. Acta Oecologica 57: 58-66 ""

  11. Ranz, J. M., Yeh S-D, Nyberg K. G., Machado C. A. (2013) Transcriptome profiling of Drosophila interspecific hybrids: insights into mechanisms of regulatory divergence and hybrid dysfunction. In “Plant Polyploidy and Hybrid Genomics” Chapter 2, p. 15-25. Z. J. Chen and J. A. Birchler, editors. John Wiley & Sons

  12. Machado C. A., Antezana M. A. (2013) Diversity, Molecular Level. In Levin S. A. (ed.) “Encyclopedia of Biodiversity 2nd Edition”, Chapter 282, Vol. 2, pp. 626-637. Waltham, MA: Academic Press. ** (Email me if you would like a reprint)

  13. Molecular Ecology Resources Primer Development Consortium, Ahanchede A., Alfaya J.E.F., Andersen L.W. et al. (2013) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2012-30 September 2012. Mol. Ecol. Res. 13:158-159

  14. Martínez-Barnetche J., Gómez-Barreto R. E., Ovilla-Muñoz M., Téllez-Sosa J. M., García López D., Dinglasan R. R., Ubaida Mohien C., MacCallum R. M., Redmond S. N., Gibbons J., Rokas A., Machado C. A., Cazares-Raga C., González-Ceron L., Hernández Martínez S., Rodríguez López M. H. (2012) Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 13: 207 (30 May 2012) doi:10.1186/1471-2164-13-207""

  15. Martinson E. O., Herre E. A., Machado C. A., Arnold A. E. (2012) Culture-free survey reveals diverse and distinctive fungal communities associated with developing figs (Ficus spp.) in Panama. Microb. Ecol. 64:1073-1084 ""

  16. Heer K., Machado C. A., Himler A., Herre E. A., Kalko E., Dick C. W. (2012) Anonymous and EST-based microsatellite DNA markers that transfer broadly across the fig tree genus (Ficus L. Moraceae). Am J. Bot. 99: e330-e333 ""

  17. Flores-Lopez C. A, Machado C. A. (2011) Analyses of 32 loci clarify phylogenetic relationships among Trypanosoma cruzi lineages and support a single hybridization prior to human contact. PLOS Negl. Trop. Dis. 5(8): e1272. ""

  18. Jiang Z-F, Croshaw D. A., Wang Y., Hey J., Machado C. A. (2011) Enrichment of mRNA-like non-coding RNAs in the divergence of Drosophila males. Mol. Biol. Evol. 28: 1339-1348 ""
  19. Himler A. G., Machado C. A. (2009) Host specificity, phenotype matching and the evolution of reproductive isolation in a coevolved plant-pollinator mutualism. Mol. Ecol. 18: 4988-4990 ""(News and Views on Smith et al.)

  20. Jiang Z-F, Machado C. A. (2009) Evolution of sex-dependent gene expression in three recently diverged species of Drosophila. Genetics 183: 1175-1185 ""(November Issue Highlight)

  21. Lopez-Vaamonde C., Winkstrom N., Kjer K. M., Weiblen G., Rasplus J-Y., Machado C. A., Cook J. M. (2009) Molecular dating and biogeography of fig-pollinating wasps. Mol. Phyl. Evol. 52: 715-726 ""

  22. Herre E. A., Jander C., Machado C. A. (2008) Evolutionary ecology of figs and their associates: ongoing progress and outstanding puzzles. Annu. Rev. Ecol. Evol. Syst. 39: 439-458 **
    ** (Email me if you would like a reprint. The publishers of Annual Reviews do not allow posting the pdf online)

  23. Schaeffer S. W. et al. (2008) Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655 ""

  24. Jackson A. P., Machado C. A., Robbins N., Herre E. A. (2008) Multi-locus phylogenetic analysis of neotropical figs does not support co-speciation with the pollinators: the importance of systematic scale in fig/wasp cophylogenetic studies. Symbiosis 45: 57-72 ""

  25. Noor M. A. F., Garfield D. A., Schaeffer S. W., Machado C. A. (2007) Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences with respect to their inversions. Genetics 177: 1417-1428 ""

  26. Drosophila 12 Genome Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218 ""

  27. Machado C. A., Matzkin L. M., Reed L., Markow T. A. (2007) Multilocus nuclear sequences reveal intra and interspecific relationships among chromosomally polymorphic species of cactophilic Drosophila. Mol. Ecol.16: 3009-3024 ""

  28. Machado C. A., Haselkorn T. S., Noor M. A. F. (2007) Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific introgression in Drosophila pseudoobscura and D. persimilis. Genetics 175: 1289-1306 ""

  29. Marussich W., Machado C. A. (2007) Host-specificity and coevolution among pollinating and non-pollinating New World fig wasps. Mol. Ecol. 16: 1925-1946 ""

  30. Vuissoz A., Worobey M., Odegaard N., Bunce M., Machado C. A., Lynnerup N., Peacock E., Gilbert M. T. P. (2007) The survival of PCR-amplifiable DNA in cow leather. J. Arch. Sci. 34: 823-829""

  31. Matzkin L. M., Watts T. D., Bitler B. G., Machado C. A., Markow T. A. (2006) Functional genomics of cactus host shifts in Drosophila mojavensis. Mol. Ecol. 15: 4635-4643 ""

  32. Ranz, J. M., Machado C. A. (2006) Uncovering evolutionary patterns of gene expression using microarrays Trends Ecol. Evol. 21: 29-37 ""

  33. Rønsted N., Weiblen G. D., Cook J. M., Salamin N., Machado C. A., Savolainen V. (2005) 60 million years of codivergence in the fig-wasp symbiosis Proc. Biol. Sci. 272: 2593-2599""

  34. Machado, C. A., Robbins, N., Gilbert, M. P. T., Herre E. A. (2005) Critical review of host specificity and its coevolutionary implications in the fig/fig-wasp mutualism. Proc. Natl. Acad. Sci. USA 102: Suppl 1:6558-65 ""

  35. Molbo D., Machado C. A., Herre E. A., Keller L. (2004) Inbreeding and population structure in two pairs of cryptic fig wasp species. Mol. Ecol. 13: 1613-1623 ""

  36. Hey J., Machado C. A. (2003) The study of structured populations: a difficult and divided science has new hope. Nature Reviews Genetics 4: 535-543""

  37. Machado C. A., Hey J. (2003) The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R. Soc. Lond. B 270: 1193-1202""

  38. Molbo, D., Machado, C. A., Sevenster, J. G., Keller L., Herre E. A. (2003) Cryptic species of fig-pollinating wasps: implications for the evolution of the fig-wasp mutualism, sex allocation, and precision of adaptation. Proc. Natl. Acad. Sci. USA 100: 5867-5872.""

  39. Machado C. A. (2003) Se cumple la regla de Hamilton? Investigación y Ciencia, November 2003""

  40. Shoemaker D. D., Machado C. A., Molbo D., Werren J. H., Windsor D. M., Herre E. A. (2002) The distribution of Wolbachia in fig wasps: correlation with host phylogeny, ecology and population structure. Proc. R. Soc. Lond. B 269: 2257-2267""

  41. Machado C. A., Ayala F. J. (2002) Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi. Mol. Biochem. Parasitol. 121: 33-47""

  42. Machado C. A., Kliman R. M., Markert J., Hey J. (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol. Biol. Evol. 19: 472-488""

  43. Noor M. A. F., Kliman R. M., Machado C. A. (2001) Evolutionary history of microsatellites in the obscura group of Drosophila. Mol. Biol. Evol. 18: 551-556""

  44. Machado C. A., Ayala F. J. (2001) Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi. Proc. Natl. Acad. Sci. USA 98: 7396-7401""

  45. Machado C. A, Jousselin E., Kjellberg F., Compton S. G., Herre E. A. (2001) Phylogenetic relationships, historical biogeography, and character evolution of fig pollinating wasps. Proc. R. Soc. Lond. B 268: 685-694""

  46. West S. A., Murray M. G., Machado C. A., Griffin A. S., Herre E. A. (2001) Testing Hamilton’s rule with competition between relatives. Nature 409: 510-513""

  47. Herre E. A, Machado C. A., West S. A. (2001) Selective regime and fig wasp sex ratios: towards sorting rigor from pseudo-rigor in tests of adaptation. In "Adaptationism and Optimality" pp. 191-218 (ed. S. Orzack & E. Sober) Cambridge University Press, New York, USA.

  48. Machado C. A., Antezana M. A. (2001) Diversity, Molecular Level. In "Encyclopedia of Biodiversity". S. Levin, Editor. Vol. 2, pp. 179-190. Academic Press, San Diego, USA.

  49. Herre E. A, Machado C. A., Bermingham E., Nason J. D., Windsor D. M., McCafferty S., Van Houten W., Bachmann K. (1996) Molecular phylogenies of figs and their pollinator wasps. J. Biogeogr. 23: 521-530""

  50. Machado C. A., Herre E. A, McCafferty S., Bermingham E. (1996) Molecular phylogenies of fig pollinating and non-pollinating wasps and the implications for the origin and evolution of the fig-fig wasp mutualism. J. Biogeogr. 23: 531-542""
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