CAS Center for Excellence in Animal Evolution and Genetics

YU Douglas W

2018-10-24 | | 【Print】

YU Douglas W, Ph.D. His major research interests are the evolution of cooperation, especially between species, and the development of efficient biodiversity monitoring methods. In 2008, he was selected as "the top scientific and technological talent of Yunnan province".

Yu has initiated and led four consortium projects in the last fifteen years, including a project using economic game theory to model the evolution of cooperation (EU EUROCORES TECT), a project to model the long-term sustainability of hunting in Manu National Park, Peru (UK Leverhulme Trust), a long-term collaboration to test screening theory on the assembly of defensive microbiomes (UK MRC, BBSRC, NERC), and a project to barcode the biodiversity of a national nature reserve in China (China, MOST).

Yu is a major participant in three current consortium projects: ArcDyn to characterize the biodiversity response to climate change (Academy of Finland), CLIMTREE to characterize the biodiversity response to forest dieback (Belmont Forum/NSFC), and a CAS Leading Directions project to carry out environmental impact analysis for the Belt and Road Initiative.

Yu has also co-founded and is scientific advisor to the UK start-up company NatureMetrics (www.naturemetrics.co.uk), which provides a variety of DNA-based methods to measure biodiversity. NatureMetrics works with a wide variety of industries and organisations to build a detailed understanding of how to protect and grow biodiversity and natural capital through adaptive management techniques in forests, farms, fisheries and beyond.

Research Interest

I work in two research areas:

High-throughput biodiversity assessment: Metabarcoding, mitogenomics, eDNA, and iDNA for biodiversity assessment and biomonitoring

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. We have been combining genomics tools with molecular taxonomy to develop methods to measure biodiversity composition and change as a function of anthropogenic pressures and natural stress gradients. Most recently, we are working on efficient metagenomic methods for characterising eukaryotic organisms, for which it is difficult to generate reference databases and difficult to measure quantitatively. Examples include pollen, nematodes, and mites.

Evolution of mutualism: emphasis on microbiomes and the application of game theory to mutualisms

To understand how multicellular organisms can evolve and enforce cooperative behavior, we adapt game theory from microeconomics. We have shown theoretically and experimentally that hosts can use a screening mechanism to assemble defensive microbiomes from the environment, that hosts primarily use pre-adaptations to punish symbiont misbehavior, that symbionts can use co-evolved password molecules to communicate reliably to hosts that they are from a mutualistic lineage, and that non-linearities in benefit functions allow groups of organisms to cooperate stably with each other to produce public goods, from diffusible molecules to cooperative hunting to sustainable management of common-pool resources.

Selected Publications

1. Kocher, S.D., Mallarino, R., Rubin, B.E.R., Yu, D.W., Hoekstra, H.E., Pierce N.E. The genetic basis for eusociality in a halictid bee. Nature Communications.

2. Heine, D., Holmes, N., Worsley, S., Alves dos Santos, A., Innocent, T., Scherlach, K., Patrick, E., Yu, D.W., Murrell, J.C., Viera, P., Boomsma, J., Hertweck, C., Hutchings, M., Wilkinson, B. (2018) Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen. Nature Communications. 9:2208. doi: 10.1038/s41467-018-04520-1.

https://theconversation.com/leafcutter-ants-are-in-a-chemical-arms-race-against-a-behaviour-changing-fungus-97892

3. Bush, A., Sollmann, R., Wilting, A., Bohmann, K., Cole, B., Balzter, H., Martius, C., Zlinszky, A., Calvignac-Spencer, S., Cobbold, C. A., Dawson, T.P., Emerson, B. C., Ferrier, S., Gilbert, M. T. P., Herold, M., Jones, L., Leendertz, F. H., Matthews, L., Millington, J. D. A., Olson, J., Ovaskainen, O., Raffaelli, D., Reeve, R., R？del, M.-O., Rodgers, T. W., Snape, S., Visseren-Hamakers, I., Vogler, A. P., White, P. C. L., Wooster, M. J., D. W. Yu. (2017) Connecting Earth Observation to High-Throughput Biodiversity Data. Nature Ecology and Evolution. 1:0176. doi: 10 .1038/s41559-017-0176.

4. Rodgers, T.W., Xu, C. C. Y., Giacalone, J., Kapheim, K. M., Saltonstall, K., Vargas, M., Yu, D. W., Somervuo, P., Jansen, P. A., McMillan, W. O. Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community. Molecular Ecology Resources. doi: 10.1111/1755-0998.12701. bioRciv: https://doi.org/10.1101/133405.

5. Cai, W., Ma, Z.X., Yang, C.Y., Wang, L., Wang, W.Z., Zhao, G.G., Geng, Y.P., Yu, D.W. (2017) Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani Rice Terrace World Heritage Site. PLoS ONE 12:e0177724–13.

6. Hua, F.Y., Wang, X.Y., Zheng, X.L. Dorazio, R.M. Fisher, B., Wang, L., Zhu, J.G., Tang, Y., Yu, D.W., and D. S. Wilcove. (2016) Opportunities for biodiversity gains under the world’s largest reforestation program. Nature Communications. 7:12717. doi:10.1038/ncomms12717

7. Zhang, K., Lin, S.L., Ji, Y.Q., Yang, C.X., Wang, X.Y., Yang, C.Y., Wang, H.S., Jiang, H.S., Harrison, R., and D.W. Yu. (2016) Plant diversity accurately predicts insect diversity in two tropical landscapes. Molecular Ecology 25:4407–4419. doi:10.1111/mec.13770. bioRciv: http://dx.doi.org/10.1101/040105

8. 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., and D.W. Yu. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods in Ecology and Evolution. 6:1034–1043.

9. Ren, G.P., Young, S., Wang, L., Wang, W., Long, Y.C., Wu, R.D., Li, J.S., Zhu, J.G., and D.W. Yu. (2015) Effectiveness of China’s National Forest Protection Program and Nature Reserves. Conservation Biology. 29:1368-1377.

10. 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/

www.takepart.com/article/2013/08/07/dna-barcoding-parasites-to-find-animals

news.mongabay.com/2014/0124-rowland-insect-soup-metabarcoding-changing-conservation.html

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

12. 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.

Included in Virtual Issue: “Top Methods in Ecology and Evolution” www.methodsinecologyandevolution.org/view/0/virtualIssues/topmethodsvirtualissue.html

13. 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.

14. 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.

15. 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