Here is a list of my publications.

Preprints

2023

Villalba de la Peña M., Summanen P. A. M., Moghadam N. N. and Kronholm I. Parental effects in a filamentous fungus: phenotype, fitness, and mechanism. Molecular Ecology, online early https://doi.org/10.1111/mec.16972

Ketola T. and Kronholm I. Experimental evolution of evolutionary potential in fluctuating environments. Journal of Evolutionary Biology, online early https://doi.org/10.1111/jeb.14178

Villalba de la Peña M., Summanen P. A. M., Liukkonen M. and Kronholm I. Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa. Genome Research 33: 1-13 https://doi.org/10.1101/gr.276992.122

2022

Bruneaux M., Ashrafi R., Kronholm I., Laanto E., Örmälä-Tiznado A.-M., Galarza J. A., Zihan C., Kubendran Sumathi M. and Ketola T. The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen. Molecular Ecology 31: 5402-5418

Kronholm I. Evolution of anticipatory effects mediated by epigenetic changes. Environmental Epigenetics 8: 1-12

Bruneaux M.*, Kronholm I.*, Ashrafi R. and Ketola T. Roles of adenine methylation and genetic mutations in adaptation to different temperatures in Serratia marcescens. Epigenetics 17: 861-881 *joint first authors

2021

Hopke A., Mela A., Ellett F., Carter-House,D., Peña J. F., Stajich J. E., Altamirano S., Lovett B., Egan M., Kale S., Kronholm I., Guerette P., Szewczyk E., McCluskey K., Breslauer D., Shah H., Coad B. D., Momany M. and Irimia D. Crowdsourced analysis of fungal growth and branching on microfluidic platforms. PLoS ONE 16: e0257823

Liukkonen M., Kronholm I. and Ketola T. Evolutionary rescue at different rates of environmental change is affected by trade-offs between short-term performance and long-term survival. Journal of Evolutionary Biology 34: 1177-1184

2020

Moghadam N. N., Sidhu K., Summanen P. A. M., Ketola T. and Kronholm I. Quantitative genetics of temperature performance curves of Neurospora crassa. Evolution 74: 1772-1787

Kronholm I., Ormsby T., McNaught K., Selker E. U. and Ketola T. Marked Neurospora crassa strains for competition experiments and Bayesian methods for fitness estimates. G3: Genes|Genomes|Genetics 10: 1261-1270

Kristensen T. N., Ketola T. and Kronholm I. Adaptation to environmental stress at different timescales. Annals of the New York Academy of Sciences 1476: 5-22

2018

Kronholm I. & Ketola T. Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments. Heredity, 121: 327-341

2017

Richards C. L., Alonso C., Becker C., Bossdorf O., Bucher E., Colomé-Tatché M., Durka W., Engelhardt J., Gaspar B., Gogol-Döring A., Grosse I., van Gurp T. P., Heer K., Kronholm I., Lampei C., Latzel V., Mirouze M., Opgenoorth L., Paun O., Prohaska S., Rensing S. A., Stadler P., Trucchi E., Ullrich K. and Verhoeven K. J. F. 2017. Ecological plant epigenetics: Evidence from model species, and the way forward. Ecology Letters 20: 1576-1590

Kronholm I. 2017. Adaptive evolution and epigenetics. In Tollefsbol T. (ed.), Handbook of Epigenetics: The New Molecular and Medical Genetics (pp. 427-438), 2nd ed., Academic Press, Cambridge. ISBN: 978-0-12-805388-1

Kronholm I., Bassett A., Baulcombe D., and Collins S. 2017. Epigenetic and genetic contributions to adaptation in Chlamydomonas. Molecular Biology and Evolution 34: 2285-2306

2016

Kronholm I., Johannesson H., Ketola T. Epigenetic control of phenotypic plasticity in the filamentous fungus Neurospora crassa. G3: Genes|Genomes|Genetics 6: 4009-4022

Kronholm I. & Collins S. 2016. Epigenetic mutations can both help and hinder adaptive evolution. Molecular Ecology 25: 1856-1868

2014

Saez-Aguayo S., Rondeau-Mouro C., Macquet A., Kronholm I., Ralet M.-C., Berger A., Sallé C., Poulain D., Granier F., Bortan L., Loudet O., de Meaux J., Marion-Poll A. & North H. M. 2014. Local evolution of seed flotation in Arabidopsis. PLoS Genetics 10: e1004221

2012

Kronholm I., Xavier F. P., Alonso-Blanco C., Goudet J. & de Meaux J. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. 2012. Evolution 66: 2287-2302

Vetter M. M., Kronholm I., He F., Häweker H., Reymond M., Bergelson J., Robatzek S. and de Meaux J. 2012. Flagellin perception varies quantitatively in Arabidopsis thaliana and its relatives. Molecular Biology and Evolution 29: 1655-1667

2011

Chiang G. C. K., Bartsch M., Barua D., Nakabayashi K., Debieu M., Kronholm I., Koornneef M., Soppe W. J. J., Donohue K., and de Meaux J. 2011. DOG1 expression is predicted by the seed-maturation environment and contributes to geographic variation in germination in Arabidopsis thaliana. Molecular Ecology 20: 3336-3349

2010

Alcázar R., García A. V., Kronholm I., de Meaux J., Koornneef M., Parker J. E. and Reymond M. 2010. Natural variation at the Strubbelig Receptor Kinase 3 drives immune-triggered incompatibilities between A. thaliana accessions. Nature Genetics 42: 1135-1139

Kronholm I., Loudet O. and de Meaux J. 2010. Influence of mutation rate on estimators of genetic differentiation – lessons from Arabidopsis thaliana. BMC Genetics 11: 33