1. He, D., Wu, R., Feng, Y., Li, Y., Ding, C. & Wang, W., Yu, D. W. 2014. China’s transboundary waters: Water and ecological security through applied ecology. Journal of Applied Ecology, 

　　2. Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Yu, D.W., de Bruyn, M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. TREE, 

　　3. Edwards, D.P., Magrach, A., Woodcock, P., Lim, N.T.L., Edwards, F.A., Larsen, T.H., Hsu, W.W., Benedick, S., Khen, C.V., Chung, A.Y.C., Hamer, K.C., Wilcove, D.S., Yu, D.W. 2014. Quantifying the biological impacts of commercial logging and forest conversion to oil palm. Ecological Applications, 

　　4. Bayliss, J., Schaafsma, M., Balmford, A., Burgess, N.D., Green, J.M.H., Madoffe, S.S., Okayasu, S., Peh, K.S-H., Platts, P.J., Yu, D.W. 2014. The current and future value of nature-based tourism in the Eastern Arc Mountains of Tanzania. Ecosystem Services, 

　　5. Kocher, S., L. Cai, Yang, W., Tan, H., Yi, S.V., Yang, X.Y., Hoekstra, H., Zhang, G.J., H. Pierce, N. E., Yu, D.W. 2013. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology, 14: R142.  

　　6. Liu, S.L., Li, Y.Y., Lu, J.L., Su, X., Tang, M., Zhou, L., Zhou, C., Yang, Q., Ji, Y.Q., Yu, D.W., and Zhou, X. 2013. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology & Evolution, 4, 1142–1150. 

　　7. Ji, Y. Q., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., Kitching, R. L., Dolman, P., Woodcock, P., Edwards, F. A., Larsen, T. H., Hsu, W. W., Benedick, S., Hamer, K. C., Wilcove, D. S., Bruce, C., Wang, X. Y., Levi, T., Lott, M., Emerson, B. C. & Yu, D. W. 2013. Reliable, verifiable, and efficient monitoring of biodiversity via metabarcoding. Ecology Letters ,16: 1245–1257.  

　　8. Seipke, R. F., J. Barke, D. Heavens, D. Yu, and M. I. Hutchings. 2013. Analysis of the bacterial communities associated with two ant-plant symbioses. Microbiology Open,,2: 276–283. 

　　9. Yu, D. W., Shepard, G. H., Ohl-Schacherer, J. & Levi, T. 2013. Resolviendo el conflicto “parque-personas” en el Manu, con la estrategia ‘Ocupar la Amazonía’. Reporte Manu 2013: Pasión por la investigación en la Amazonía Peruana (eds. J. Groenendijk, A. Tovar & W. Wust), pp. 342–368. San Diego Zoo Global Peru y SERNANP, Lima, Peru. 

　　10. Ramirez-Gonzalez, R., D. W. Yu, C. Bruce, D. Heavens, M. Caccamo, and B. C. Emerson 2013. PyroClean: Denoising pyrosequences from protein coding amplicons for the recovery of interspecific and intraspecific genetic variation. PLoS ONE, 8: e57615. 

　　11. Beckschäfer, P., P. Mundhenk, C. Kleinn, Y. Ji, D.W. Yu and R.D. Harrison. 2013. Enhanced structural complexity index: an improved index for describing forest structural complexity. Open Journal of Forestry, 3:23-29. 

　　12. Wang, H., J. Ridley, D. W. Dunn, R. W. Wang, J. M. Cook, and D. W. Yu. 2013. Biased oviposition and biased survival together help resolve a fig-wasp conflict. Oikos ,122:533–540. 

　　13. Scheuring, I., Yu, D.W. 2012. How to assemble a beneficial microbiome in three easy steps. Ecology Letters, 15:1300-1307. 

　　14. Yu, D.W., Ji, Y.Q., Emerson, B.C., Ding, Z.L., Wang, X.Y., Yang, C.Y., Ye, C.X. 2012. Biodiversity soup: Metabarcoding for rapid, large-scale biodiversity assessment and biomonitoring of arthropods. Methods in Ecology & Evolution, 3:613–623. 

　　15. Shepard, G.H., Levi, T. Neves, E.G., Peres, C.A., Yu, D.W. 2012. Hunting in ancient and modern Amazonia: Rethinking sustainability. American Anthropologist, 114: 652–667.  

　　16. Ye, C., Z. S. Ma, C. H. Cannon, M. Pop, and D. W. Yu. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics, 13:S1. 

　　17. Archetti, M., Scheuring, I., Hoffman, M., Frederickson, M.E., Pierce, N.E., Yu, D.W. 2011. Economic game theory for mutualism and cooperation. Ecology Letters, 14: 1300-1312. 

　　18. Seipke, R.F., Barke, J., Ruiz-Gonzalez, M.X., Orivel, J., Yu, D.W., Hutchings, M.I. 2011. Fungus-growing Allomerus ants are associated with antibiotic-producing Actinobacteria. Antonie van Leeuwenhoek, 101:443–447. 

　　19. Seipke R.F., Barke J., Brearley C., Hill L., Yu D.W., Goss R.J.M. & Hutchings M.I. 2011. A single Streptomyces mutualist makes multiple antifungals to support the fungus farming ant Acromyrmex octospinosus. PLoS ONE, 6: e22028. 

　　20. Dunn, D. W., S. Jansen-González, J. M. Cook, D. W. Yu, and R. A. S. Pereira. 2011. Measuring the discrepancy between fecundity and lifetime reproductive success in a pollinating fig wasp. Entomologia Experimentalis Et Applicata, 140:218-225. 

　　21. Levi, T., Lu, F., Yu, D.W., Mangel, M. 2011. The behavior and diet breadth of central-place foragers: an application to human hunters and Neotropical game management. Evolutionary Ecology Research, 13: 171–185. 

　　22. Levi, T., Shepard Jr., G.H., Ohl-Schacherer, J., Wilmers, C., Peres, C.A., Yu, D.W. 2011. Spatial tools for modeling the sustainability of subsistence hunting in tropical forests. Ecological Applications, 21: 1802-1818. 

　　23. Wu R., Zhang S., Yu D.W., Zhao P., Li X., Wang L., Yu Q., Ma J., Chen A. & Long Y. 2011.. Effectiveness of China’s nature reserves in representing ecological diversity. Frontiers in Ecology and the Environment, 9: 383-389.  

　　24. Kirkby, C., Giudice, R., Day, B., Turner, R.K., Soares-Filho, B.F., Oliveira-Rodrigues, H., Yu, D.W. 2011. Closing the ecotourism-conservation loop in Amazonian Peru. Environmental Conservation, 38: 6-17. 

　　25. Archetti, M., Ubeda, F., Fudenberg, D., Green, J., Pierce, N.E., Yu, D.W. 2011. Let the right one in: a microeconomic approach to partner choice in mutualisms. American Naturalist. 177: 75-85. （Faculty of 1000 Exceptional Paper, f1000.com/10426957） 

　　26. Barke, J., Seipke, R.F., Yu, D.W., Hutchings, M.I. 2011. A mutualistic microbiome: How do fungus-growing ants select their antibiotic-producing bacteria? Invited addendum in Communicative & Integrative Biology 4: 1-3. 

　　27. Weyl, E.G., Frederickson, M.E., Yu, D.W., Pierce, N.E. 2010. Economic contract theory tests models of mutualism. Proceedings of the National Academy of Sciences USA 107: 15712–15716.（Faculty of 1000 Must Read Paper, f1000biology.com/article/id/1282068） 

　　28. Barke, J., Seipke, R.F., Gruschow, S., Heavens, D., Drou, N., Bibb, M.J., Goss, R.J.M., Yu, D.W., Hutchings, M.I., 2010. A mixed community of actinomycetes produces multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC Biology 8: 109.  

　　29. Kirkby, C., Giudice, R., Day, B., Turner, R.K., Velarde-Andrade, L.-M., Dueñas-Dueñas, A., Lara-Rivas, J.-C., Yu, D.W. 2010. The market triumph of ecotourism: An economic investigation of the private and social benefits of competing land uses in the Peruvian Amazon. PLoS ONE 5, e13015. 

　　30. Yu, D.W., Levi, T., Shepard, G.H. 2010. Conservation in low-governance environments. Biotropica, 42: 569-571. 

　　31. Bawa, K.S., Koh, L. P. Lee, T.M., Liu, J., Ramakrishnan, P.S., Yu, D.W. , Zhang, Y.-P., Raven, P.H. 2010. China, India, and the environment. Science, 327: 1457-1458.  

　　32. Debout, G. D. G., Frederickson, M., Aron, S., Yu, D.W. 2010. Unexplained split sex ratios in the Neotropical symbiotic plant-ant, Allomerus octoarticulatus var. demerarae (Myrmicinae): a test of hypotheses. Evolution, 64: 126-141.  

　　33. Kirkby, C., Giudice, R., Day, B., Turner, R.K., Soares-Filho, B.F., Oliveira-Rodrigues, H., Yu, D.W. 2010. Closing the ecotourism-conservation loop in Amazonian Peru. In The Theory and Practice of Ecosystem Service Valuation (eds. P. M. Kareiva, T. H. Ricketts, G. C. Daily, H. Tallis, & S. Polasky) Cambridge U. Press.  

　　34. Kirkby, C. & D.W. Yu. 2010. Ecotourism case study. In Introduction to Tropical Rain Forest Ecology and Management (eds. J. Ghazoul & D. Sheil) Oxford U. Press.  

　　35. Shepard, G.H., Rummenhoeller, K., Ohl-Schacherer, J., Yu, D.W. 2010. Trouble in Paradise: Indigenous populations, anthropological policies, and biodiversity conservation in Manu National Park, Peru. Journal of Sustainable Forestry 29: 252–301. 

　　36. Abraão M.B., Shepard Jr, G.H., Nelson B.W., Baniwa J.C., Andrello G., Yu, D.W. 2010. Baniwa habitat classification in the white-sand campinarana habitat of the Northwest Amazon. pp. 83-115 in Landscape ethnoecology: concepts of biotic and physical space (eds. L. M. Johnson & E.S. Hunn) Berghahn Books (New York).  

　　37. Yu, D.W. 2010. Managing the exploitation of wildlife in tropical forests. pp. 121-123 in Conservation Biology for All (eds. N. S. Sodhi & P. R. Ehrlich) Oxford U. Press. 

　　38. Endo, W., Salas, E., Mori, S. Pacheco, V., Peres, C., Yu, D.W. 2010. Game vertebrate densities in hunted and nonhunted forest sites in Manu National Park, Peru. Biotropica ,42: 251-261.  

　　39. Palminteri, S., G. Powell, W. Endo, C. Kirkby, D. W. Yu, and C. A. Peres. 2009. Usefulness of species range polygons in representing a primate community in southeastern Peru. American Journal of Primatology, 71: 1-9.  

　　40. Wang, R.W., Ridley, J., Shi, L., Dunn, D.W., Cook, J.M., Zhang, Y.-P., Yu, D.W. 2009. Interference competition and high temperature reduce the virulence of fig wasps and stabilize a fig-wasp mutualism. PLoS One, 4: e7802. （Faculty of 1000 Recommended Paper, f1000biology.com/article/id/1282068） 

　　41. Edwards, D.P., Frederickson, M.E., Shepard, G.H., Yu, D.W. 2009. ‘A plant needs ants like a dog needs fleas:’ Myrmelachista schumanni ants gall many tree species to create housing. American Naturalist, 174: 734-740.  

　　42. Szilágyi, A., Scheuring, I., Orivel, J., Edwards, D.P., Yu, D.W. 2009. The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment. Ecology Letters, 12: 1306-1316. （Faculty of 1000 Recommended Paper, www.f1000biology.com/article/id/1968966） 

　　43. Levi, T., Shepard Jr., G.H., Ohl-Schacherer, J., Peres, C.A., Yu, D.W. 2009. Modeling the long-term sustainability of indigenous hunting in Manu National Park, Peru: Landscape-scale management implications for Amazonia. Journal of Applied Ecology ,46: 804-814.（Selected by Journal of Applied Ecology as one of the twenty-one most influential papers on applied forest management and global change in the last five years, and one of four of the most influential papers on sustainable harvest） 

　　44. Fisher, B., K. Turner, M. Zylstra, R. Brouwer, R. de Groot, S. Farber, P. Ferraro, R. Green, D. Hadley, J. Harlow, P. Jefferiss, C. Kirkby, P. Morling, S. Mowatt, R. Naidoo, J. Paavola, B. Strassburg, D. Yu, and A. Balmford. 2008. Ecosystem services and economic theory: integration for policy-relevant research. Ecological Applications, 18: 2050-2067.（Faculty of 1000 Must Read Paper, f1000.com/1163989） 

　　45. Edwards, D.P. and Yu, D.W. Tolerating castration by hiding flowers in plain sight. 2008. Behavioral Ecology and Sociobiology, 63: 95-102. 

　　46. Abraão, M., Baniwa, J.C., Nelson, B.W., Andrello, G., Yu, D.W. & Shepard, G.H. 2008. Ethnobotanical Ground-Truthing of Baniwa Landscape Knowledge in the White-Sand Campinarana Forests of the Upper Rio Negro, Brazil. Journal of Biogeography, 35: 2237-2248. 

　　47. Dunn, D., Yu, D.W., Ridley, J., Cook, J.M. 2008. Longevity, size and early emergence in a pollinating fig wasp – implications for the stability of the fig-pollinator mutualism. Journal of Animal Ecology, 77: 927-935. 

　　48. Bush, A.A., Yu, D.W., Herberstein, M.E. 2008. Function of bright colouration in the Wasp Spider Argiope bruennichi (Araneae: Araneidae). Proceedings of the Royal Society of London B, 275: 1337-1342. 

　　49. Ohl-Schacherer, J., Mannigel, E., Kirkby, C., Shepard Jr., G.H., Yu, D.W. 2008. Indigenous ecotourism in the Amazon: A case study of ‘Casa Matsiguenka’ in Manu National Park, Peru. Environmental Conservation, 35: 14-25.  

　　50. Dunn, D. W., S. T. Segar, J. Ridley, R. Chan, R. H. Crozier, D. W. Yu, and J. M. Cook. 2008. A role for parasites in stabilising the fig-pollinator mutualism. PLoS Biology, 6:490-496. 

　　51. Yu, D.W., Proulx, S.M., Shepard, G.H. 2008. Masculinity, marriage and the paradox of the lek. pp. 88-107 in The Body Beautiful (eds. V. Swami & A. Furnham). New York: Palgrave Macmillan.  

　　52. Ohl, J., Wezel, A., Shepard Jr., G.H., Yu, D.W. 2007. Swidden agriculture in a human-inhabited protected area: The Matsigenka native communities of Manu National Park, Peru. Environment, Development, and Sustainability, 10: 827-843. 

　　53. Edwards, D.P., R. Arauco, M. Hassall, W. J. Sutherland, K. Chamberlain, L. J. Wadham, and D. W. Yu. 2007. Protection in an ant-plant mutualism: an adaptation or a sensory trap? Animal Behaviour, 74: 377-385. 

　　54. Ohl-Schacherer, J., Shepard Jr., G.H., Kaplan, H., Peres, C.A., Levi, T., Yu, D.W. 2007. The sustainability of hunting by Matsigenka native communities in Manu National Park, Peru. Conservation Biology, 21: 1174-1185. 

　　55. Edwards, D.P. & Yu, D.W. 2007. The roles of sensory traps in the origin, maintenance, and breakdown of mutualism. Behavioral Ecology and Sociobiology, 61:1321-1327. 

　　56. Debout, G. D. G., Ventelon-Debout, G., Emerson, B. C. & Yu, D. W. 2007. PCR primers for polymorphic microsatellite loci in the plant-ant Azteca ulei var. cordiae (Formicidae: Dolichoderinae). Molecular Ecology Notes, 7: 607-609. 

　　57. da Silva, M.N., Shepard Jr., G.H., Yu, D.W. 2005, appeared in 2007. Conservation implications of primate hunting practices among the Matsigenka of Manu National Park. Neotropical Primates, 13: 31-36.  

　　58. Debout, G. D. G., Pereyra, R., Emerson, B. C. & Yu, D. W. 2006. Characterisation of polymorphic microsatellites in the castration parasite plant-ant Allomerus octoarticulatus cf. demerarae (Formicidae: Myrmicinae). Molecular Ecology Notes, 6: 182-184.  

　　59. Edwards, D.P., Arauco, R., Hassall, M., Sutherland, W.J., Yu, D.W. 2006. Assembling a mutualism: ant symbionts locate their host plants by detecting volatile chemicals. Insectes Sociaux,, 53: 172-176. 

　　60. Edwards, DP, M Hassall, WJ Sutherland and DW Yu 2006.. Selection for protection in ant-plant mutualism: host sanctions, host modularity, and the principal-agent game. Proceedings of the Royal Society of London B, 273: 595-602. 

　　61. Ridley, J, DW Yu and WJ Sutherland. 2005..Why long-lived species are more likely to be social: the role of local dominance. Behavioral Ecology, 16: 358-363. 

　　62. Yu D.W., Wilson H.B., Frederickson M.E., Palomino W., De la Colina R., Edwards D.P. & Balareso A.A.. 2004. Experimental demonstration of species coexistence enabled by dispersal limitation. Journal of Animal Ecology 73, 1102-1114. (Faculty of 1000 Recommended Paper, f1000biology.com/article/id/1022217) 

　　63. Yu, D. W., J. Ridley, E. Jousselin, E. A. Herre, S. G. Compton, J. M. Cook, J. C. Moore, G.D. Weiblen. 2004. Oviposition strategies, host coercion, and the stable exploitation of figs by wasps. Proceedings of the Royal Society of London B, 271, 1185–1195. 

　　64. Shepard, G.H., D.W. Yu, B. Nelson, M. Lizarralde & M. Italiano. 2004. Ethnobotanical Ground-Truthing and Forest Diversity in the Western Amazon. In Ethnobotany and conservation of biocultural diversity (eds. L. Maffi, T. Carlson and E. López-Zent). New York: New York Botanical Gardens (Advances in Economic Botany). 

　　65. Peres, C.A., Baider, C., Zuidema, P.A., Wadt, L.H.O., Kainer, K.A., Gomes-Silva, D.A.P., Salomão, R.P., Simões, L.L., Franciosi, E.R.N., Cornejo, F., Gribel, R., Shepard, G.H., Kanashiro, M., Coventry, P., Yu, D.W., Watkinson, A.R., & Freckleton, R.P. 2003. Demographic threats to the sustainability of Brazil nut exploitation. Science, 302, 2112-2114. 

　　66. Yu, D.W., W. J. Sutherland, and C. Clark. 2002. Trade versus environment. TREE, 17:341-344. 

　　67. Yu, D. W., and J. Ridley. 2003. Geopolitics in a buttercup. TREE,18:163-165. 

　　68. Shepard Jr., G. H., & D. W. Yu. 2001. Verificación etnobotánica de imágenes de satélite: La intersección de conocimientos tradicionales y cientifícos. Debate Agrario, 33: 19-24. 

　　69. Yu, D. W., H. B. Wilson, N. E. Pierce. 2001. An empirical model of species coexistence in a spatially structured environment. Ecology, 82: 1761–1771..  

　　70. Yu, D. W. & H. B. Wilson. 2001. The competition-colonization tradeoff is dead. Long live the competition-colonization tradeoff American Naturalist, 158: 49–63. 

　　71. Yu, D. W. 2001. Parasites of mutualisms. Biological Journal of the Linnean Society, 72: 529–546. 

　　72. Shepard Jr., G., D. W. Yu, M. Lizarralde, and M. Italiano. 2001. Rain forest habitat classification among the Matsigenka of the Peruvian Amazon. Journal of Ethnobiology, 21: 1-38.  

　　73. Weiblen, G. D., D. W. Yu, and S. A. West. 2001. Pollination and parasitism in functionally dioecious figs. Proceedings of the Royal Society of London B, 268: 651-659. 

　　74. Plotkin, J.B., M.D. Potts, D.W. Yu, S. Bunyvejchewin, R. Condit, R. Foster, S. Hubbell, J. LaFrankie, N. Manokaran, L.H. Seng, R. Sukumar, M.A. Nowak & P.S. Ashton. 2000. Predicting species diversity in tropical forests. Proceedings of the National Academy of Sciences USA, 97: 10850-10854.  

　　75.Yu, D.W. & G.H. Shepard. 1999. The mystery of female beauty: Reply. Nature, 399: 216.  

　　76.Yu, D.W. & G.H. Shepard. 1998. Is beauty in the eye of the beholder?  Nature, 396: 321-322.  

　　77.Yu, D.W., J.W. Terborgh & M.D. Potts. 1998. Can high tree species richness be explained by Hubbell's null model? Ecology Letters, 1: 193-199.  

　　78.Yu, D. W., and N. E. Pierce. 1998. A castration parasite of an ant-plant mutualism. Proceedings of the Royal Society of London B, 265: 375-382.  

　　79. Shea, K., Amarasekare, P., Kareiva, P., Mangel, M., Moore, J., Murdoch, W. W., Noonburg, E., Parma, A. M., Pascual, M. A., Possingham, H. P., Wilcox, C. & Yu, D., 1998. Management of populations in conservation, harvesting and control. TREE, 13, 371-374.  

　　80. Parma, A. M., Amarasekare, P., Mangel, M., Moore, J., Murdoch, W. W., Noonburg, E., Pascual, M. A., Possingham, H. P., Shea, K., Wilcox, C. & Yu, D. 1998. What can adaptive management do for our fish, forests, food, and biodiversity? Integrative Biology, 1: 6-26.  

　　81. Yu, D. W. & D. Quicke. 1997. Compsobraconoides (Braconidae: Braconinae), the first Hymenopteran ectoparasitoid of adult Azteca ants (Hymenoptera: Formicidae). Journal of Hymenoptera Research, 6: 419-421. 

　　82. Yu, D. W., T. Hendrickson & A. Castillo. 1997. Ecotourism in Peru: short-term and long-term challenges. Environmental Conservation, 24: 130-138.  

　　83. Yu, D.W. & D. W. Davidson. 1997. Experimental studies of species-specificity in Cecropia-ant relationships. Ecological Monographs, 67: 273-294.  

　　84. Terborgh, J. W., L. Lopez, J. Tello, D. W. Yu & A. R. Bruni. 1997. Transitory states in relaxing ecosystems of land-bridge islands. Pp. 256-274 in Tropical Forest Remnants: Ecology, Management, and Conservation of Fragmented Communities. (W. F. Laurance and R. O. Bierregaard, Jr., Eds., University of Chicago Press, Chicago).  

　　85. Yu, D. W. 1995. New factor in free trade: Reply to Jenkins. Conservation Biology, 10: 303-304. 

　　86. Yu, D. W. 1994. Free trade is green. Protectionism is not. Conservation Biology, 8: 989-996. 

　　87. Yu, D. W. 1994. The structural role of epiphytes in ant gardens. Biotropica, 26: 222-226.