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Tang, M., Hardman, C.J., Ji, Y.Q., Meng, G.L., Liu, S.L., Tan, M.H., Yang, S.Z., Moss, E.D., Yang, C.X., Bruce, C., Nevard, T., Potts, S.G., Zhou, X., Yu, D.W. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution.

Ren, G.P., Young, S., Wang W., Wang, L., Yu, D.W., Zhu, J.G. (2015) Effectiveness of China’s National Forest Protection Program and Nature Reserves. Conservation Biology

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 51:1159-1168.

Gao H., Grüschow S., Barke J., Seipke R.F., Hill L.M., Orivel J., Yu D.W., Hutchings M.I. & Goss R.J.M. (2014) Filipins: the first antifungal “weed killers” identified from bacteria isolated from the trap-ant. RSC Advances 4:57267–57270.

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) Selective-logging and oil palm: multitaxon impacts, biodiversity indicators, and trade-offs for conservation planning. Ecological Applications 24:2029–2049.

Scott, I. M., Josephson, S. C., Boyette, A., Clark, A. P., Fried, R., Gibson, M., Hewlett, B., Jamieson, M., Jankowiak, W., Honey, P. L., Huang, Z., Liebert, M. A., Purzycki, B. G., Shaver, J., Sosis, R., Snodgrass, J. J., Sugiyama, L. S., Swami, V., Yu, D. W., Zhao, Y. & Penton-Voak, I. S. (2014) Human preferences for sexually dimorphic faces may be evolutionarily novel. Proceedings of the National Academy of Sciences USA 111:14388-14393.

Harris, R.B., Zhou, J.K., Ji, Y.Q., Kai, Z., Yang, C.Y., Yu, D.W. (2014) Evidence that the Tibetan fox is an obligate predator of the plateau pika: conservation implications. Journal of Mammalogy 95:1207-1221.

Yang, C.X., Wang, X.Y., Miller, J.A., de Blécourt, M., Ji, Y.Q., Yang C.Y., Harrison, R.D., Yu, D.W. (2014) Using metabarcoding to ask if easily collected soil and leaf-litter fauna can be used as a general biodiversity indicator. Ecological Indicators 46:379-389.

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 29:358–367.

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 8:75-83.

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.

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.

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.

www.cosmosmagazine.com/features/leech-rangers-patrol-the-jungle/

Seipke RF, J Barke, D Heavens, D Yu and MI Hutchings (2013) Analysis of the bacterial communities associated with two ant-plant symbioses. MicrobiologyOpen 2: 276-283.

Ramirez-Gonzalez R, DW Yu, C Bruce, D Heavens, M Caccamo and BC Emerson (2013) PyroClean: Denoising pyrosequences from protein coding amplicons for the recovery of interspecific and intraspecific genetic variation. PLoS ONE 8: 57615e.

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.
English language version ("Resolving the people-park conflict in Manu with the Occupy Amazon strategy") available on academia.edu


Beckschäfer P, P Mundhenk, C Kleinn, Y Ji, DW Yu and RD Harrison (2013) Enhanced structural complexity index: an improved index for describing forest structural complexity. Open Journal of Forestry 3: 23-29.

Wang H, J Ridley, DW Dunn, RW Wang, JM Cook and DW Yu (2013) Biased oviposition and biased survival together help resolve a fig-wasp conflict. Oikos 122: 533–540.

Scheuring I, and DW Yu (2012) How to assemble a beneficial microbiome in three easy steps. Ecology Letters 15: 1300-1307.

Ye C, ZS Ma, CH Cannon, M Pop and DW Yu (2012) Exploiting sparseness in de novo genome assembly. BMC Bioinformatics 13 (Suppl 6): S1.

Yu DW, Y Ji, BC Emerson, X Wang, C Ye, C Yang and Z Ding (2012) Biodiversity soup:metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution 3: 613–623.

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.

Levi T, GH Shepard, J Ohl-Schacherer, CC Wilmers, CA Peres and DW Yu (2011) Spatial tools for modeling the sustainability of subsistence hunting in tropical forests. Ecological Applications 21: 1802-1818.

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

Barke J, RF Seipke, DW Yu and MI Hutchings (2011) A mutualistic microbiome: How do fungus-growing ants select their antibiotic-producing bacteria? Communicative & Integrative Biology 4: 1-3.

Archetti M, F Úbeda, D Fudenberg, J Green, NE Pierce and DW Yu (2011) Let the right one in: a microeconomic approach to partner choice in mutualisms. The American Naturalist 177: 75-85.

Yu DW, T Levi and GH Shepard (2010) Conservation in low-governance environments. Biotropica 42: 569–571.

Weyl EG, ME Frederickson, DW Yu and NE Pierce (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/5674972


Barke J, RF Seipke, S Gruschow, D Heavens, N Drou, MJ Bibb, RJM Goss, DW Yu and MI Hutchings (2010) A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC Biology 8:109. [BMC Highly Accessed]

Kirkby CA, B Day, K Turner, BS Soares-Filho, H Oliveira and DW Yu (2011) Closing the ecotourism-conservation loop in the Peruvian Amazon. Environmental Conservation 38:6-17.

Kirkby C, R Giudice, B Day, RK Turner, LM Velarde-Andrade, A Dueñas-Dueñas, JC Lara-Rivas and DW Yu (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.

Bawa KS, LP Koh, TM Lee, J Liu, PS Ramakrishnan, DW Yu, Y-P Zhang and PH Raven (2010) China, India, and the Environment. Science 327: 1457-1458.

Wang RW, J Ridley, L Shi, DW Dunn, JM Cook, Y-P Zhang and DW Yu (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
 

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

Kirkby C, R Giudice, B Day, RK Turner, B-F Soares-Filho, H Oliveira-Rodrigues and DW Yu (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.

Shepard GH, K Rummenhoeller, J Ohl and DW Yu. (2010) Trouble in Paradise: Indigenous populations, anthropological policies, and biodiversity conservation in Manu National Park, Peru. Journal of Sustainable Forestry.

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

Edwards DP, ME Frederickson, GH Shepard and DW Yu (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.

Szilágyi A, I Scheuring, J Orivel, DP Edwards and DW Yu (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 http://f1000biology.com/article/id/1968966


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

Endo W, E Salas, S Mori, V Pacheco, C Peres and DW Yu (2009) Game vertebrate densities in hunted and nonhunted forest sites in Manu National Park, Peru.  Biotropica  42: 251-261.

Levi T, GH Shepard Jr., J Ohl-Schacherer, CA Peres and DW Yu (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.

Yu DW (2010) Managing the exploitation of wildlife in tropical forests.  In Conservation Biology for All (eds. N. S. Sodhi & P. R. Ehrlich) Oxford U. Press.

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, DW Yu and A Balmford (2009) Integrating Ecosystem Services and Economic Theory: what can we do, what should we do, and what has been done? Ecological Applications 18: 2050-2067.

Edwards DP and DW Yu (2008) Tolerating castration by hiding flowers in plain sight. Behavioral Ecology and Sociobiology 63: 95-102.

Bush AA, DW Yu and ME Herberstein (2008) Function of bright colouration in the Wasp SpiderArgiope bruennichi (Araneae: Araneidae). Proceedings of the Royal Society of London B 275: 1337-1342.

Dunn D, J Ridley, JM Cook and DW Yu (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.

Dunn D, ST Segar, J Ridley, R Chan, RH Crozier, DW Yu and Cook, J.M. (2008) A role for parasites in stabilising the fig-pollinator mutualism.  PLoS Biology 6: 490-496.

Ohl-Schacherer J, E Mannigel, C Kirkby, GH Shepard Jr. and DW Yu (2008) Ecotourism and sustainable development in indigenous communities – A case study from Manu National Park, Peru. Environmental Conservation 35: 14-25.

Abraão M, GH Shepard, BW Nelson, JC Baniwa, G Andrello and DW Yu (2010) Baniwa Vegetation Classification in the White-Sand Campinarana Habitat of the Northwest Amazon Pages 83-115 in Landscape Ethnoecology (eds. L.M. Johnson & E. Hunn). New York:  Berghahn Books.

Abraão M, JC Baniwa, BW Nelson, G Andrello, DW Yu and GH Shepard (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.

Yu DW, SM Proulx, and GH Shepard Jr. (2008)  Masculinity, marriage and the paradox of the lek. pp. 88-107 in The Body Beautiful (eds. V. Swami & A. Furham). New York:  Palgrave Macmillan.

Ohl J, A Wezel, GH Shepard Jr. and DW Yu (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.

Edwards DP, R Arauco, M Hassall, WJ Sutherland, K Chamberlain, LJ Wadham and DW Yu (2007) Protection in an ant-plant mutualism:  an adaptation or a sensory trap? Animal Behaviour 74: 377-385.

Ohl-Schacherer J, GH Shepard Jr., H Kaplan, CA Peres, T Levi and DW Yu (2007) The sustainability of hunting by Matsigenka native communities in Manu National Park, Peru. Conservation Biology 21:  1174-1185.

Edwards DP and DW Yu (2007) The roles of sensory traps in the origin, maintenance, and breakdown of mutualism. Behavioral Ecology and Sociobiology 61: 1321-1327.

Debout GDG, G Ventelon-Debout, BC Emerson and DW Yu (2007) PCR primers for polymorphic microsatellite loci in the plant-ant Azteca ulei var. cordiae (Formicidae: Dolichoderinae). Molecular EcologyNotes  7:  607-609.

da Silva MN, GH Shepard Jr. and DW Yu (2005, out in 2007) Conservation implications of primate hunting practices among the Matsigenka of Manu National Park. Neotropical Primates 13(2): 31-36.

Debout GDG, R Pereyra, BC Emerson and DW Yu (2006) Characterisation of polymorphic microsatellites in the castration parasite plant-ant Allomerus octoarticulatus cf. demerarae (Formicidae: Myrmicinae). Molecular Ecology Notes 6: 182-184.

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

Edwards DP, M Hassall, WJ Sutherland and DW Yu (2006) Assembling a mutualism: ant symbionts locate their host plants by detecting volatile chemicals. Insectes Sociaux 53: 172-176.

Yu DW (2005) Seeking evidence of God's work undermines faith. (Correspondence). Nature 435: 275-276.

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.

Yu DW, HB Wilson, ME Frederickson, W Palomino, R De la Colina, AA Balareso and DP Edwards. (2004) Experimental demonstration of species coexistence enabled by dispersal limitation. Journal of Animal Ecology. 73: 1102-1114.
Faculty of 1000 Recommended Paper http://f1000biology.com/article/id/1022217
 

Yu DW, J Ridley, E Jousselin, EA Herre, SG Compton, JM Cook, JC Moore and GD Weiblen (2004) Optimal foraging, host coercion, and the stable exploitation of figs by wasps. Proceedings of the Royal Society of London B 271, 1185–1195.

Shepard GH, DW Yu, B Nelson, M Lizarralde and 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).

Peres, CA, C Baider, PA Zidema, LHO Wadt, KA Kainer, DAP Gomes-Silva, RP Salomão, LL Simões, ERN Franciosi, F Cornejo, R Gribel, GH Shepard, M Kanashiro, P Coventry, DW Yu, AR Watkinson and RP Freckleton (2003) Demographic threats to the sustainability of Brazil nut exploitation. Science 302, 2112-2114.

Yu DW and J Ridley (2003) Geopolitics in a buttercup. TREE 18:163-165.

Yu DW, WJ Sutherland and C Clark (2002) Trade versus environment. TREE 17:341-344.

Shepard Jr. GH and DW Yu (2002) Vanishing Cultures (Comment). NY Review of Books 50: 92.

Shepard Jr. GH and DW Yu (2001) Verificación etnobotánica de imágenes de satélite: La intersección de conocimientos tradicionales y cientifícos. Debate Agrario 33: 19-24.

Yu DW, Wilson HB, and NE Pierce (2001) An empirical model of species coexistence in a spatially structured environment. Ecology 82: 1761–1771.

Yu DW and HB Wilson (2001) The competition-colonization tradeoff is dead; long live the competition-colonization tradeoff. American Naturalist 158: 49–63.

Yu DW (2001) Parasites of mutualisms. Biological Journal of the Linnean Society 72: 529–546.

Shepard Jr. G, DW Yu, M Lizarralde and M Italian (2001) Rain forest habitat classification among the Matsigenka of the Peruvian Amazon. Journal of Ethnobiology 21: 1-38.

Weiblen GD, DW Yu and SA West (2001) Pollination and parasitism in functionally dioecious figs. Proceedings of the Royal Society of London B 268: 651-659.

Plotkin JB, MD Potts, DW Yu, S Bunyvejchewin, R Condit, R Foster, S Hubbell, J LaFrankie, N Manokaran, LH Seng, R Sukumar, MA Nowak and PS Ashton (2000) Predicting species diversity in tropical forests. Proceedings of the National Academy of Sciences USA, 97: 10850-10854.

Yu DW and GH Shepard (1999) The mystery of female beauty: Reply. Nature 399: 216.

Yu DW and GH Shepard (1998) Is beauty in the eye of the beholder? Nature 396: 321-322.

Yu DW, JW Terborgh and MD Potts (1998) Can high tree species richness be explained by Hubbell's null model? Ecology Letters 1: 193-199.

Yu DW and NE Pierce (1998) A castration parasite of an ant-plant mutualism. Proceedings of the Royal Society of London B 265: 375-382.

Shea K, P Amarasekare, P Kareiva, M Mangel, J Moore, WW Murdoch, E Noonburg, AM Parma, MA Pascual, HP Possingham, C Wilcox and DW Yu (1998) Management of populations in conservation, harvesting and control. TREE 13: 371-374.

Parma AM, P Amarasekare, M Mangel, J Moore, WW Murdoch, E Noonburg, MA Pascual, HP Possingham, K Shea, C Wilcox and D Yu (1998) What can adaptive management do for our fish, forests, food, and biodiversity? Integrative Biology 1: 6-26.

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

Yu DW, T Hendrickson and A Castillo (1997) Ecotourism in Peru: short-term and long-term challenges. Environmental Conservation 24: 130-138.

Yu DW and DW Davidson (1997) Experimental studies of species-specificity in Cecropia-ant relationships. Ecological Monographs 67: 273-294.

Terborgh JW, L Lopez, J Tello, DW Yu and AR 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.

Yu, DW (1995) New factor in free trade: Reply to Jenkins. Conservation Biology 10: 303-304.

Yu, DW (1994) Free trade is green. Protectionism is not. Conservation Biology 8: 989-996.

Yu, DW (1994) The structural role of epiphytes in ant gardens. Biotropica 26: 222-226.