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Rike StelkensAssociate Professor

About me

My lab is an international group of evolutionary biologists. Together, we investigate how populations evolve to adapt to environmental stress. We are especially interested in the genetic and phenotypic responses of populations to life in deteriorating or poor quality environments. For this, we use the microbe Baker’s yeast (or budding yeast – Saccharomyces cerevisiae) and its wild relatives as a model system, and a combination of experimental evolution and next generation sequencing. We generate populations that range in genetic variation from clonal (i.e. only genetically identical individuals at first) to extremely diverse (i.e. hybrid swarms made from crossing different species). We propagate these populations for hundreds of generations in stressful environments, using experimental evolution. This allows us to watch the evolutionary process unfold in the lab. We use fitness assays and genome sequencing on these lab-evolved strains from different time points of their frozen “fossil record”, which allows us to parse the contributions of the four population genetic processes – mutation, genetic drift, recombination and selection – to understand what drives the dynamics of adaptation.

Luckily, yeast comes with its own genetic toolkit and great high quality reference genomes, plus it can reproduce asexually and sexually, which makes it a great system to study the different drivers of evolutionary adaptation.

Some of the questions we are currently working on:

  • What is the genetic architecture of fitness and adaptation under environmental stress?
  • How likely is parallel evolution when populations adapt from standing genetic variation?
  • How do the type and rate of environmental change affect adaptation dynamics?
  • What is the evolutionary significance of structural genomic variation (e.g. aneuploidy), and how does it affect hybrid fitness?
  • Is the distribution of fitness effects (DFE) comparable across environments and systems? This is a collaboration with some great colleagues at the Math Dept (Chun-Biu Li).
  • We’re also working with insects! Together with David Berger at Uppsala University, we are looking at temperature adaptation and the evolution of phenotypic plasticity in seed beetles (Callosobruchus maculatus).

If you are interested in any of the above or related questions, please drop me an email.

 

Grants and Sponsors:

Vetenskapsrådet

Knut and Alice Wallenberg Foundation

Carl Tryggers Stiftelse 

Science for Life Laboratories

Erik Philip-Sörensens Stiftelse

Wenner Gren Foundations

Stockholm University

Royal Physiographic Society of Lund

 

Publications:

  1. Ament-Velásquez* L, C Gilchrist*, A Rêgo, DP Bendixsen, C Brice, J Grosse-Sommer, N Rafati, R Stelkens. The dynamics of adaptation to stress from standing genetic variation and de novo mutations. Molecular Biology and Evolution, 2022, https://doi.org/10.1093/molbev/msac242, *authors contributed equally
  2. Stelkens R, DP Bendixsen: The evolutionary and ecological potential of yeast hybrids. Current Opinion in Genetics & Development 2022, 76:101958 https://doi.org/10.1016/j.gde.2022.101958
  3. Tavakolian N, JG Frazão, DP Bendixsen, R Stelkens, CB Li : Shepherd: accurate clustering for correcting DNA barcode errors. Bioinformatics 2022, 38:3710-3716 https://doi.org/10.1093/bioinformatics/btac395
  4. Gettle N, Gallone B, Verstrepen K, Stelkens R. 2022. Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines. bioRxiv, 2022, doi: https://doi.org/10.1101/2022.03.17.484703
  5. Boynton PJ, Patil KR, Stefanini I, Stelkens R, Cubillos FA, Yeast ecology and communities. Yeast, 2022, 39(1-2):3.
  6. Bendixsen DP, JG Frazão, R Stelkens, Saccharomyces yeast hybrids on the rise, Yeast, 2021, https://doi.org/10.1002/yea.3684
  7. Bendixsen DP, D Peris, R Stelkens. Patterns of genomic instability in interspecific yeast hybrids with diverse ancestries, Frontiers in Fungal Biology, 2021, https://www.frontiersin.org/articles/10.3389/ffunb.2021.742894/abstract
  8. Bendixsen DP, N Gettle, C Gilchrist, Z Zhang, R Stelkens, Genomic evidence of an ancient East Asian divergence event in wild Saccharomyces cerevisiae. Genome Biology and Evolution, 2021, evab001, https://doi.org/10.1093/gbe/evab001
  9. Meier JI, RB Stelkens, DA Joyce, S Mwaiko, N Phiri, UK Schliewen, OM Selz, CE Wagner, C Katongo, O Seehausen, The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes, Nature Communications, 2019, 10:5391. https://www.nature.com/articles/s41467-019-13278-z
  10. Zhang Z*, DP Bendixsen*, T Janzen, AW Nolte, D Greig, RB Stelkens, Recombining your way out of trouble: The genetic architecture of hybrid fitness under environmental stress, Molecular Biology and Evolution, 2019, https://doi.org/10.1093/molbev/msz211; *authors contributed equally
  11. Gilchrist C, RB Stelkens, Aneuploidy in Yeast: Segregation Error or Adaptation Mechanism? Yeast, 2019, https://doi.org/10.1002/yea.3427
  12. Bernardes J, RB Stelkens, D Greig, Heterosis in hybrids within and between yeast species, Journal of Evolutionary Biology, 2017, 30 (3): 538–548 doi: 10.1111/jeb.13023
  13. Stelkens RB, D Greig, Fungal evolution: On the origin of yeast species, NATURE Microbiology 2016, 1 (1): 15017, doi: 10.1038/nmicrobiol2015.17
  14. Boynton P, RB Stelkens, V Kowallik, D Greig, Measuring microbial fitness in a field reciprocal transplant experiment, Molecular Ecology Resources, 2016, doi: 10.1111/1755-0998.12562
  15. Stelkens RB, EL Miller, D Greig, Asynchronous spore germination in isogenic, natural isolates of Saccharomyces paradoxus, FEMS Yeast Research, 2016, 16 (3) doi: 10.1093/femsyr/fow012
  16. Stelkens RB*, K King*, J Webster, D Smith, M Brockhurst, Hybridization in parasites: Consequences for adaptive evolution, pathogenesis, and public health in a changing world, PLOS Pathogens, 2015, 11(9): e1005098 *authors contributed equally
  17. Stelkens RB, C. Schmid, O Seehausen, Hybrid breakdown in cichlid fish, PLOS ONE, 2015, 10(5): e0127207
  18. Stelkens RB, M Brockhurst, G Hurst, E Miller, D Greig, The effect of hybrid transgression on environmental tolerance in experimental yeast crosses. Journal of Evolutionary Biology, 2014, 27(11): 2507-2519
  19. Stelkens RB, M Brockhurst, G Hurst, D Greig, Hybridization facilitates evolutionary rescue, Evolutionary Applications, 2014, 7(10): 1209-1217
  20. Stelkens RB, M Pompini, C Wedekind, Testing the effects of genetic crossing distance on embryo survival within a metapopulation of brown trout (Salmo trutta). Conservation Genetics, 2014, 15: 375-386
  21. Stelkens RB*, ES Clark*, C Wedekind, Parental influences on pathogen resistance in brown trout embryos and effects of outcrossing within a river network, PLOS ONE, 2013, 8: e57832 *authors contributed equally
  22. Stelkens RB, M Pompini, C Wedekind, Testing for local adaptation in brown trout using reciprocal transplants. BMC Evolutionary Biology, 2012, 12: 247
  23. Abbott R, D Albach, S Ansell, JW Arntzen, SJE Baird, N Bierne et al. (incl. RB Stelkens), Hybridization and speciation. Journal of Evolutionary Biology, 2012, 26: 229-246
  24. Stelkens RB, G Jaffuel, M Escher, C Wedekind, Genetic and phenotypic population divergence on a microgeographic scale in brown trout. Molecular Ecology, 2012, 21:2896-2915
  25. Stelkens RB, C Wedekind, Environmental sex reversal, Trojan sex genes, and sex ratio adjustment: conditions and population consequences. Molecular Ecology, 2010, 19: 627–646
  26. Wedekind C, RB Stelkens, Tackling the diversity of sex determination. Biology Letters, 2010, 6: 7-9
  27. Stelkens RB, KA Young, O Seehausen, The accumulation of reproductive incompatibilities in African cichlid fish. Evolution, 2010, 64:617-633
  28. Stelkens RB, C Schmid, O Selz, O Seehausen, Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish. BMC Evolutionary Biology, 2009, 9:283, doi: 10.1186/1471-2148-9-283
  29. Stelkens RB, O Seehausen, Genetic distance between species predicts novel trait expression in their hybrids. Evolution, 2009, 63:884-897
  30. Stelkens RB, O Seehausen, Phenotypic divergence but not genetic distance predicts assortative mating among species of a new cichlid fish radiation. Journal of Evolutionary Biology, 2009, 22:1679-1694
  31. Stelkens RB, MER Pierotti, DA Joyce, AM Smith, I van der Sluijs, O Seehausen, Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish. Philosophical Transactions of the Royal Society B-Biological Sciences, 2008, 363:2861-2870
  32. van der Sluijs I, TJM Van Dooren, KD Hofker, JJM van Alphen, RB Stelkens, O Seehausen, Female mating preference functions predict sexual selection against hybrids between sibling species of cichlid fish. Philosophical Transactions of the Royal Society B-Biological Sciences, 2008, 363:2871-2877
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