Dr. Douglas W. Yu Yu’s research can be called “Management Theory for Biology.” How do hosts manage their symbionts when symbiont behaviour and characteristics cannot be fully observed? How can society manage our biological heritage for the benefit of the many, when the same society exploits natural resources for private economic benefits, and moreover, when the exploitation is difficult to observe and control? In this light, Yu’s group has spent their time on two areas:

(1) Developing and testing game-theoretical models of symbiosis, especially microbiomes. We are using screening and public-goods game-theory models (Archetti et al. 2011) to explain how the leafcutter ant is able to recruit mainly (or only) antibiotic-producing actinobacteria from the soil environment, despite the vast diversity of bacteria that live in the soil. Actinobacteria-dominated microbiomes are found across the kingdoms of life, from plant rhizosphere to corals to insects to birds, and even form a component of the human gut. The advantage of the leafcutter system is that it is possible to use molecular-genetic tools to create actinobacterial species with suites of traits that we have identified as leading to different microbiome outcomes, to inoculate ants with them in the lab, and then to assay whether the bacteria survive and which natural products are being secreted. Our overall goal is to develop an empirically tested theory of microbiomes, which will have utility for a range of applications, from natural products discovery to health management to crop protection.

(2) Developing ‘metabarcoding’ techniques to accelerate biodiversity assessments. The arthropods make up well over half of the world’s named species, are targets for conservation in their own right, and can be used for monitoring environmental conditions. The problem is taxonomic identification. We are using next-generation sequencing to mass-barcode slurries of mass-trapped arthropods. Ultimately, our goal is to make rapid and large-scale assessments of the state of the environment with a broad, efficient, and legally defensible measure of biodiversity instead of indicators, which are of inherently uncertain reliability. Such measures can be used for a variety of environmental management problems, from pollution monitoring to agri-environment schemes, to systematic conservation planning, to fundamental studies of evolution and ecology.

Yu has more than 80 publications, including in Nature, Science, PNAS, PLoS Biology, Ecology Letters, Ecological Monographs, Ecology, American Naturalist, Evolution, J. Applied Ecology, J. Animal Ecology, Conservation Biology, and Proceedings of the Royal Society of London B.

E-mail: dougwyu@gmail.com

Reliable, verifiable and efficient monitoring of biodiversity via Metabarcoding

Yinqiu Ji,Louise Ashton, Scott M. Pedley, David P.Edwards,Yong Tang,Akihiro Nakamura, Roger Kitching, Paul M. Dolman, Paul Woodcock, Felicity A. Edwards, Trond H. Larsen, Wayne W. Hsu, Suzan Benedick, Keith C. Hamer, David S. Wilcove, Catharine Bruce, Xiaoyang Wang, Taal Levi, Martin Lott, Brent C. Emerson and Douglas W. Yu

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.

Biaed oviposition and biased survival together help resolve a fig–wasp conflict

Hui Wang, Jo Ridley, Derek W. Dunn, Ruiwu Wang, James M. Cook and Douglas W. Yu

We report evidence that helps resolve two competing explanations for stability in the mutualism between Ficus racemosa fig trees and the Ceratosolen fusciceps wasps that pollinate them. The wasps lay eggs in the tree’s ovules, with each wasp larva developing at the expense of a fig seed. Upon maturity, the female wasps collect pollen and disperse to a new tree, continuing the cycle. Fig fitness is increased by producing both seeds and female wasps, whereas short-term wasp fitness increases only with more wasps, thereby resulting in a conflict of interests. We show experimentally that wasps exploit the inner layers of ovules first (the biased oviposition explanation), which is consistent with optimal-foraging theory. As oviposition increases, seeds in the middle layer are replaced on a one-to-one basis by pollinator offspring, which is also consistent with biased oviposition. Finally, in the outer layer of ovules, seeds disappear but are only partially replaced by pollinator offspring, which suggests high wasp mortality (the biased survival or ‘unbeatable seeds’ explanation). Our results therefore suggest that both biased oviposition and biased survival ensure seed production, thereby stabilizing the mutualism. We further argue that biased oviposition can maintain biased survival by selecting against wasp traits to overcome fig defenses. Finally, we report evidence suggesting that F. racemosa balances seed and wasp production at the level of the tree. Because figs are probably selected to allocate equally to male and female function, a 1:1 seed:wasp ratio suggests that fig trees are in control of the mutualism.

Highlights Publications in 2013  

1.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. doi:10.1186/gb-2013-14-12-r142          

2.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.

3.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.  

4.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.

5.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.

6.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.

Lab Staff:

Dr. Zhu Jianguo, Associate Researcher, zhu@mail.kiz.ac.cn

Dr. Ji Yinqiu, Assistant Researcher, jiyinqiu@hotmail.com

Dr. Yang Chunyan, Assistant Researcher, yangyahan@mail.kiz.ac.cn

Mr. Wang Lin, Research Assistant, wang174344@163.com

Ms.Wang Jiaxin, Research Assistant, wanglin@mail.kiz.ac.cn

Ms. Wu Chunying, Research Assistant, wuchunying1011@163.com

Graduate Students:

Yang Chenxue, Zhang Kai, Wang Xiaoyang, Yu Longlong, Catharine Powell