Rike StelkensUniversitetslektor

Om mig

Our 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:

• How does environmental change, including global warming, affect adaptation dynamics?
• What is the genetic architecture of adaptive traits?
• How do thermal performance curves (TPCs) evolve?
• How likely is parallel evolution in increasingly divergent populations/species?
• How do structural genomic variants (e.g. having extra chromosomes) affect fitness?

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. Molinet J, R Stelkens, The evolution of thermal performance curves in response to rising temperature across the model genus yeast, PNAS, 2025 (accepted for publication)
2. Rêgo A, J Baur, C Girard-Tercieux, M de la Paz Celorio Mancera, R Stelkens, D Berger, Repeatability of evolution and genomic predictions of temperature adaptation in seed beetles. Nature Ecology & Evolution, 2025 (accepted for publication)
3. 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, 2024, https://www.nature.com/articles/s41467-024-54105-4
4. Stelkens R, A microbial perspective on speciation. Evolutionary Journal of the Linnean Society, 2024, doi.org/10.1093/evolinnean/kzae023
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. 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
7. 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.
8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. Boynton PJ, Patil KR, Stefanini I, Stelkens R, Cubillos FA, Yeast ecology and communities. Yeast, 2022, 39(1-2):3.
16. Bendixsen DP, JG Frazão, R Stelkens, Saccharomyces yeast hybrids on the rise, Yeast, 2021, https://doi.org/10.1002/yea.3684
17. 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
18. 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
19. 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
20. 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
21. 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
22. Gilchrist C, RB Stelkens, Aneuploidy in Yeast: Segregation Error or Adaptation Mechanism? Yeast, 2019, https://doi.org/10.1002/yea.3427
23. 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
24. Stelkens RB, D Greig, Fungal evolution: On the origin of yeast species, NATURE Microbiology 2016, 1 (1): 15017, doi: 10.1038/nmicrobiol2015.17
25. 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
26. 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
27. 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
28. Stelkens RB, C. Schmid, O Seehausen, Hybrid breakdown in cichlid fish, PLOS ONE, 2015, 10(5): e0127207
29. 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
30. Stelkens RB, M Brockhurst, G Hurst, D Greig, Hybridization facilitates evolutionary rescue, Evolutionary Applications, 2014, 7(10): 1209-1217
31. 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
32. 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
33. Stelkens RB, M Pompini, C Wedekind, Testing for local adaptation in brown trout using reciprocal transplants. BMC Evolutionary Biology, 2012, 12: 247
34. 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
35. 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
36. Stelkens RB, C Wedekind, Environmental sex reversal, Trojan sex genes, and sex ratio adjustment: conditions and population consequences. Molecular Ecology, 2010, 19: 627–646
37. Wedekind C, RB Stelkens, Tackling the diversity of sex determination. Biology Letters, 2010, 6: 7-9
38. Stelkens RB, KA Young, O Seehausen, The accumulation of reproductive incompatibilities in African cichlid fish. Evolution, 2010, 64:617-633
39. 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
40. Stelkens RB, O Seehausen, Genetic distance between species predicts novel trait expression in their hybrids. Evolution, 2009, 63:884-897
41. 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
42. 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
43. 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