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The genetic basis of adaptive evolution


Project Description

A unique study system (the micro-crustacean Daphnia) is used to identify the mechanisms of adaptation to environmental change. These include epigenetics enabling phenotypic plasticity that may precede and inform the genetic fixation of adaptive traits. The environmental genomics model organism Daphnia produces diapausing embryos as part of its reproductive cycle. When buried in the lake sediments, these embryos produce a living archive of past populations that can be sampled and resuscitated in the laboratory after prolonged periods of time. Investigators at the University of Birmingham have hatched these dormant embryos to resume development, producing healthy reproductive adults, even after 700 years of sustained developmental arrest. From these hatchlings, populations of Daphnia are indefinitely maintained in the laboratory for evolutionary studies through 10,000 generations. Using an “evolutionary genetic” panel consisting of Daphnia populations resuscitated from a lake sediment spanning 100 years of ecological change, the student will apply quantitative genetic theory to detect the genetic basis for plasticity in gene expression and functional gene-gene associations under multiple environmental conditions. Transcriptional and epigenetic quantitative traits are a promising frontier in Daphnia. In other species, this work reveals that variation in the abundance of gene transcripts is an important class of quantitative traits, and that a considerable fraction of gene expression is heritable. There is increasing evidence that quantitative trait loci (QTLs) associated with phenotypes of interest are more likely to be expression QTLs (eQTLs) than allelic variation for other genomic elements at equal frequencies. Most recently, a new class of QTLs called variance QTLs (or veQTLs) has been discovered, which are genetic determinants of observed variability in gene expression. veQTLs are revealed by conducting experiments capable of partitioning variance among individuals (e.g. recombinant inbred lines, or Daphnia clonal isolates) that have the same or different genomic backgrounds. Detection of such veQTLs is important to understand adaptive evolution, because differences in veQTLs at a locus can either result from epistasis among genetically interacting loci, from genotype-by-environment interactions, or both. In all cases, these interactions produce context-dependent effects, and may themselves be targets of natural selection contributing to the adaptive potential of natural populations.
This project is closely associated with other research at the University of Birmingham and beyond that focuses on the study of diapausing Daphnia populations buried in lake sediments so to uniquely witness the molecular mechanisms of adaptive evolution in natural populations over decades and centuries against the documented environmental changes that have occurred from local to regional scales (called resurrection biology). As such, partners and collaborators include the Natural History Museum (ancient DNA research), the UK MetOffice (climate change), Natural England and the Environment Agency (biodiversity in the face of pollutants).
Any questions about the project can be directed to: Professor John Colbourne -

Funding Notes

CENTA studentships are for 3.5 years and are funded by NERC. In addition to the full payment of their tuition fees, successful candidates will receive the following financial support:

Annual stipend, set at £14,777 for 2018/19
Research training support grant (RTSG) of £8,000

References

Nogués-Bravo D. Rodríguez-Sánchez F., L. Orsini, E. de Boer, R. Jansson, H. Morlon, D. Fordham and S. Jackson. 2018. Cracking the code of past biodiversity responses to climate change. Trends in Ecology and Evolution 33: 765-776.

Kvist, J., C.G. Athanàsio, O.S. Solari, J.B. Brown, J.K. Colbourne, M.E. Pfrender and L. Mirbahai. 2018. Pattern of DNA methylation in Daphnia: Evolutionary perspective. Genome Biology and Evolution, evy155, https://doi.org/10.1093/gbe/evy155.

Frisch, D., P.K. Morton, P. Roy Chowdhury, B.W. Culver, J.K. Colbourne, L.J. Weider and P.D. Jeyasingh. 2014. A millennial-scale chronicle of evolutionary responses to cultural eutrophication in Daphnia. Ecology Letters 17: 360–368.

Colbourne, J.K., M.E. Pfrender, D. Gilbert, W.K. Thomas, et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.

Ayroles J.F, M.A. Carbone, E.A. Stone, K.W. Jordan, R.F. Lyman, M.M. Magwire, S.M. Rollmann, L.H. Duncan, F. Lawrence, R.R. Anholt and T.F. Mackay. 2009. Systems genetics of complex traits in Drosophila melanogaster. Nature Genetics 41(3): 299-307.
Cheung V.G., L.K. Conlin, T.M. Weber, M. Arcaro, K.Y. Jen, M. Morley, R.S. Spielman. 2003. Natural variation in human gene expression assessed in lymphoblastoid cells. Nature Genetics 33(3): 422-225.
Zhang X., A.J. Cal and J.O. Borevitz and D.L. Nicolae. 2011. Genetic architecture of regulatory variation in Arabidopsis thaliana. Genome Research 21(5): 725-733.

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