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, whole genome sequencing, transcriptomics, and phenotyping. We work with populations that range in genetic variation from clonal (i.e. only genetically identical individuals) to extremely diverse (i.e. hybrid swarms made from crossing different species). We propagate these populations for hundreds of generations in diverse environments, which allows us to watch evolution in action. Using time-series analysis of the fitness and genome of our frozen 'fossil records', we 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, including hybridization.

Some of the questions we are currently working on:

• What is the genetic architecture of fitness and adaptation in diverse and complex environments?
• 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?
• 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. Stelkens R, A microbial perspective on speciation. Evolutionary Journal of the Linnean Society, 2024, doi.org/10.1093/evolinnean/kzae023
2. Bautista C, I Gagnon-Arsenault, M Utrobina, A Fijarczyk, DP Bendixsen, R Stelkens, C Landry, Hybrid adaptation is hampered by Haldane’s sieve, Nature Communications (in print) (preprint on biorxiv, 2023,doi.org/10.1101/2023.12.15.571924)
3. Molinet J, JP Navarrete, CA Villarroel, P Villarreal, FI Sandoval, RF Nespolo, R Stelkens, FA Cubillos, Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for Lager brewing. PLOS Genetics, 2024, e1011154, 10.1371/journal.pgen.1011154
4. Rêgo A, J Baur, C Girard-Tercieux, M de la Paz Celorio Mancera, R Stelkens, D Berger, Strong selection but low repeatability: temperature-specific effects on genomic predictions of adaptation. biorxiv, 2024, doi.org/10.1101/2024.09.12.612579
5. Pinto J, R Stelkens, The long-term evolutionary potential of four yeast species and their hybrids in extreme temperature conditions, biorxiv, 2024, doi.org/10.1101/2024.09.27.615317
6. Rêgo, A, D Stajic, C Bautista, S Rouot, M de la Paz Celorio-Mancera, R Stelkens, Adaptation to complex environments reveals pervasive trade-offs and genomic targets with large pleiotropic effects, bioRxiv, 2024: p. 2024.01.24.577006.
7. Pinto, J, N Tavakolian, CB Li, R Stelkens, The relationship between cell density and cell count differs among Saccharomyces yeast species. microPublication Biology, 2024. 10.17912/micropub.biology.001215
8. Thompson KA, Y Brandvain, JM Coughlan, KE Delmore, H Justen, C Linnen, D Ortiz-Barrientos, CA Rushworth, H Schneemann, M Schumer, R Stelkens, The Ecology of Hybrid Incompatibilities, Cold Spring Harbour Perspectives in Biology, 2023, a041438
9. Delmore K, H Justen, KM Kay, J Kitano, LC Moyle, R Stelkens, MA Streisfeld, YY Yamasaki, J Ross, Genomic approaches are improving taxonomic representation in genetic studies of speciation, Cold Spring Harbour Perspectives in Biology, 2023, doi:10.1101/cshperspect.a041438
10. 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
11. 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
12. 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
13. 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
14. Boynton PJ, Patil KR, Stefanini I, Stelkens R, Cubillos FA, Yeast ecology and communities. Yeast, 2022, 39(1-2):3.
15. Bendixsen DP, JG Frazão, R Stelkens, Saccharomyces yeast hybrids on the rise, Yeast, 2021, https://doi.org/10.1002/yea.3684
16. 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
17. Brice C, Z Zhang, DP Bendixsen, R Stelkens. 2021. Hybridization outcomes have strong genomic and environmental contingencies. The American Naturalist, 2021, doi.org/10.1086/715356
18. 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
19. 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
20. 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
21. Gilchrist C, RB Stelkens, Aneuploidy in Yeast: Segregation Error or Adaptation Mechanism? Yeast, 2019, https://doi.org/10.1002/yea.3427
22. 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
23. Stelkens RB, D Greig, Fungal evolution: On the origin of yeast species, NATURE Microbiology 2016, 1 (1): 15017, doi: 10.1038/nmicrobiol2015.17
24. 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
25. 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
26. 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
27. Stelkens RB, C. Schmid, O Seehausen, Hybrid breakdown in cichlid fish, PLOS ONE, 2015, 10(5): e0127207
28. 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
29. Stelkens RB, M Brockhurst, G Hurst, D Greig, Hybridization facilitates evolutionary rescue, Evolutionary Applications, 2014, 7(10): 1209-1217
30. 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
31. 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
32. Stelkens RB, M Pompini, C Wedekind, Testing for local adaptation in brown trout using reciprocal transplants. BMC Evolutionary Biology, 2012, 12: 247
33. 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
34. 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
35. Stelkens RB, C Wedekind, Environmental sex reversal, Trojan sex genes, and sex ratio adjustment: conditions and population consequences. Molecular Ecology, 2010, 19: 627–646
36. Wedekind C, RB Stelkens, Tackling the diversity of sex determination. Biology Letters, 2010, 6: 7-9
37. Stelkens RB, KA Young, O Seehausen, The accumulation of reproductive incompatibilities in African cichlid fish. Evolution, 2010, 64:617-633
38. 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
39. Stelkens RB, O Seehausen, Genetic distance between species predicts novel trait expression in their hybrids. Evolution, 2009, 63:884-897
40. 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
41. 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
42. 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