PhD Research Project: Forecasting species persistence to future global change by learning from past

Overview
Eutrophication and climate change are two most pressing environmental issues affecting 30-40% of freshwater lakes and reservoirs worldwide 1, 2, and reducing provision of water resource 3, biodiversity 4 and other services such as tourism and recreation 5, 6. Deterioration of inland waters typically arises from a combination of excess nutrient input and a breakdown in grazers’ trophic control, with profound implications for ecosystem structure and function 7. Lakes’ historical records show that changes in nutrient inputs can induce transitions between eutrophic and oligotrophic states and that regulation of nutrient loads can lead to a return to clear water conditions 8, 9. While a great deal of work has focused on these environmental transitions in the context of regime shifts 10, 11, by coupling the transitions with the evolutionary dynamics of keystone grazers12, drivers of community dynamics, we can gain robust insights into whether the grazer might persist and evolve through environmental shifts and contribute to the persistence, rather than breakdown, of aquatic ecosystem services under climate change.
The keystone grazers Daphnia spp offer the unique opportunity to ‘resurrect’ historical populations from lake sediment13, providing us with the ability to reconstruct the evolution of a key player in the grazing community through environmental transitions and to reveal the relative importance of plasticity and evolution in persistent community structure and ecosystem service.

Objectives:
Objective 1: to reconstruct the evolutionary response of the keystone grazer Daphnia to past shifts from oligotrophic to eutrophic conditions and to document its persistence under realistic global change scenarios.
Objective 2: to uncover the molecular and metabolic processes underpinning evolutionary responses to eutrophication and climate change
Objective 3: to link fitness responses to the genetic and metabolic processes that ensure species persistence to global change.
Capitalizing on the well-defined role of Daphnia spp. in sustaining freshwater ecosystems 14, 15 and its unique life cycle that enables us to perform common garden experiments on ancestral (extinct) and modern populations, we will gain unprecedented insights into natural patterns of evolution and into how history of local adaptation can orchestrate a response to future climate change.

Methodology
Objective 1: Using ‘resurrection ecology’ we will resurrect specimens of the keystone aquatic grazer Daphnia magna from lakes with known history of eutrophication and temperature changes. Extinct and modern populations will be used in common garden experiments to document fitness changes that occurred in response to past and that will occur under future environmental shifts.
Objective 2: Using multiomics approaches we will characterize the genome, transcriptome and metabolome of resurrected populations to disentangle the interplay between phenotypic plasticity and genetic adaptation in the response to global change.
Objective 3. Using advanced computational tools and biostatistic approaches we will perform a cutting-edge integrative analysis of multiomics and fitness data to uncover the genetic and metabolic elements driving adaptation to global change and ensuring species persistence.

Training and skills
CENTA students complete 45 days training throughout their PhD including a 10 day placement.
The supervisor team, collectively, has a long track record of graduate and postgraduate supervision. The DR will receive multisciplinary training by this supervisor team spanning from evolutionary biology, multiomics technologies, advanced computational and biostatistics skills. The DR will have access to the NERC Biomolecular Analysis Facility for Metabolomics and the Joint Centre for Environmental Omics, providing him/her with training in the most up to date ‘omics’ technologies. Moreover he/she will have access to one of the largest Daphnia facilities in England managed by a specialized technician who provides hands-on training for undergraduate and graduate students.

Possible timeline:
Year 1: Resurrect Daphnia magna specimens from lake sediment (material available); establish isoclonal cultures; perform common garden experiments exposing resurrected lines to environmental conditions that mimic historical environmental shifts to uncover evolutionary mechanisms driving adaptation; perform common garden experiments mimicking realistic future global change scenarios to assess species persistence to future global change. Collect tissue for multiomics.
Year 2: Obtain genomic, transcriptomic and metabolomic data.
Year 3: Perform integrative analysis of multiomics and fitness data to be published in one large or two smaller chapters in year 4. This integrative analysis will require advanced computational and biostatistic skills.

Funding Notes

please refer to the CENTA webpage http://www.centa.org.uk/themes/anthropogenic/b5/

References

1. Ansari AA, Gill SS, Lanza GR, Rast W. Eutrophication: Causes, Consequences and Control. Springer: Dordrecht, Heidelberg, London, New York, 2011.
2. Foley JA, DeFries R, Asner GP, Barford C, Bonan G, Carpenter SR, et al. Global consequences of land use. Science 2005, 309(5734): 570-574.
3. Posch T, Koster O, Salcher MM, Pernthaler J. Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming. Nature Climate Change 2012, 2(11): 809-813.
4. Ferriere R, Dieckmann U, Couvet D. Evolutionary conservation biology. Cambridge University Press: Cambridge, UK, 2004.
5. Dodds WK, Bouska WW, Eitzmann JL, Pilger TJ, Pitts KL, Riley AJ, et al. Eutrophication of U.S. Freshwaters: Analysis of Potential Economic Damages. Amrican Chemical Society 2009, 43: 12-19.
6. Dokulil MT. Environmental Impacts of Tourism on Lakes Eutrophication: Causes, Consequences and Control. Springer Netherlands, 2014, pp 81-88.
7. Chislock MF, Doster E, Zitomer RA, Wilson AE. Eutrophication: Causes, Consequences, and Controls in Aquatic Ecosystems. Nature Education Knowledge 2013, 4: 10.
8. Sayer C, Burgess A, Kari K, Davidson A, Peglar S, Yang H, et al. Long-term dynamics of submerged macrophytes and algae in a small and shallow, eutrophic lake: implications for the stability of macrophyte-dominance. Freshwater Biol 2010, 55: 565-583.
9. Sayer CD, Davidson TA, Jones JI, Langdon PG. Combining contemporary ecology and palaeolimnology to understand shallow lake ecosystem change. Freshwater Biol 2010, 55: 487-499.
10. Carpenter SR. Regime shifts in lake ecosystems: pattern and variation. Oldendorf/Luhe: Germany, 2003.
11. Scheffer M, Jeppesen E. Regime Shifts in Shallow Lakes. Ecosystems 2007, 10: 1.
12. Orsini L, Schwenk K, De Meester L, Colbourne JK, Pfrender ME, Weider LJ. The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. Trends in Ecology and Evolution 2013, 28: 274-282.
13. Kerfoot WC, Weider LJ. Experimental paleoecology (resurrection ecology): Chasing Van Valen’s Red Queen hypothesis. Limnol Oceanogr 2004, 49(4): 1300-1316.
14. Altshuler I, Demiri B, Xu S, Constantin A, Yan ND, Cristescu ME. An integrated multi-disciplinary approach for studying multiple stressors in freshwater ecosystems: Daphnia as a model organism. Integr Comp Biol 2011, 51(4): 623-633.
15. Miner BE, De Meester L, Pfrender ME, Lampert W, Hairston NG. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. P Roy Soc B-Biol Sci 2012, 279(1735): 1873-1882.