Collecting cod eggs. Photo credit: Espen Bierud
THEMES and tools
adaptation | plasticity | behaviour
gene flow | structural variation | mating systems | reproductive barriers
common garden experiments | mating experiments
genomics | transcriptomics | bioacoustics | telemetry
bioinformatics | modelling | artificial intelligence | network science
gene flow | structural variation | mating systems | reproductive barriers
common garden experiments | mating experiments
genomics | transcriptomics | bioacoustics | telemetry
bioinformatics | modelling | artificial intelligence | network science
Atlantic cod; Photo: Emilie Reuchlin-Hugenholtz
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Gene expression network of the stress response
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Spectrogram of a cod mating call
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RESEARCH TOPICS
[SCROLL DOWN FOR PUBLICATION LIST]
Phenotypic plasticity & reaction norm evolution
The slope and shape of a reaction norm represents the plastic response of a genotype to the environment (Oomen & Hutchings 2020). Differences in reaction norm intercepts, slopes, or shapes between genotypes can represent divergent evolutionary responses to previous environments and, consequently, divergent responses to current and future changes in the environment (Oomen & Hutchings 2015a, 2016). Outstanding questions in reaction norm evolution stimulate my research group to understand the spatial and temporal scales at which divergent reaction norms occur, how differences in plasticity are maintained by local adaptation in the face of gene flow, and the genomic basis of adaptation in plasticity (Oomen & Hutchings 2015b, 2017). These questions are critical for our understanding of current and future distributions of marine biodiversity in a changing world (Oomen & Hutchings 2022).
The slope and shape of a reaction norm represents the plastic response of a genotype to the environment (Oomen & Hutchings 2020). Differences in reaction norm intercepts, slopes, or shapes between genotypes can represent divergent evolutionary responses to previous environments and, consequently, divergent responses to current and future changes in the environment (Oomen & Hutchings 2015a, 2016). Outstanding questions in reaction norm evolution stimulate my research group to understand the spatial and temporal scales at which divergent reaction norms occur, how differences in plasticity are maintained by local adaptation in the face of gene flow, and the genomic basis of adaptation in plasticity (Oomen & Hutchings 2015b, 2017). These questions are critical for our understanding of current and future distributions of marine biodiversity in a changing world (Oomen & Hutchings 2022).
The genomic basis of local adaptation with gene flow
Dissecting the roles of sequence and structural genomic variation in adaptation and diversification is of increasing interest in evolutionary ecology since chromosome-level genome assemblies became more widely available (Mérot, Oomen et al. 2020). Theory suggests that high gene flow, which is common in the marine environment, favours adaptation driven by large-effect loci and blocks of loci with reduced recombination (e.g., chromosomal inversions, supergenes), which prevent advantageous allelic combinations from being split up (Oomen et al. 2020). However, recent large-scale sequencing efforts in fishes have also implicated polygenic architectures in rapid and stable speciation in sympatry. The conditions under and the extent to which different genomic architectures contribute to adaptation and diversification of marine taxa are open questions that my research group pursues.
Dissecting the roles of sequence and structural genomic variation in adaptation and diversification is of increasing interest in evolutionary ecology since chromosome-level genome assemblies became more widely available (Mérot, Oomen et al. 2020). Theory suggests that high gene flow, which is common in the marine environment, favours adaptation driven by large-effect loci and blocks of loci with reduced recombination (e.g., chromosomal inversions, supergenes), which prevent advantageous allelic combinations from being split up (Oomen et al. 2020). However, recent large-scale sequencing efforts in fishes have also implicated polygenic architectures in rapid and stable speciation in sympatry. The conditions under and the extent to which different genomic architectures contribute to adaptation and diversification of marine taxa are open questions that my research group pursues.
Ecological & genomic mechanisms of speciation at sea
Reproductive isolating mechanisms, such as assortative mating and hybrid inviability, are the primary defence in the face of gene flow that can swamp locally adapted alleles. Hybrid zones, where genetically distinct forms interact, represent natural laboratories for studying barriers to gene flow. The coexistence of genetically distinct ecotypes of Atlantic cod raises the question of how divergent ecotypes are maintained in the face of potential interbreeding (Roney, Oomen et al. 2018; Oomen et al. 2021). We explore the roles of mating vocalisations and hybrid viability in reproductive success and ecotype maintenance, ultimately aimed at identifying the genomic basis of the persistence of hybridizing ecotypes as discrete entities. In doing so, we will identify the dynamic roles of natural and sexual selection in determining the persistence of sympatric ecotypes and their consequences in a changing world.
Reproductive isolating mechanisms, such as assortative mating and hybrid inviability, are the primary defence in the face of gene flow that can swamp locally adapted alleles. Hybrid zones, where genetically distinct forms interact, represent natural laboratories for studying barriers to gene flow. The coexistence of genetically distinct ecotypes of Atlantic cod raises the question of how divergent ecotypes are maintained in the face of potential interbreeding (Roney, Oomen et al. 2018; Oomen et al. 2021). We explore the roles of mating vocalisations and hybrid viability in reproductive success and ecotype maintenance, ultimately aimed at identifying the genomic basis of the persistence of hybridizing ecotypes as discrete entities. In doing so, we will identify the dynamic roles of natural and sexual selection in determining the persistence of sympatric ecotypes and their consequences in a changing world.
OVERARCHING GOAL: Genomic forecasting
Genome sequencing, eco-evolutionary modelling, and genetic simulations are unlocking the potential for genomic forecasts of population, species, and ecosystem responses to environmental change (Oomen & Hutchings 2022). Simulations show that single locus control of a life history trait under harvest-induced selection generates a more variable evolutionary response compared to an unlinked polygenic scenario (Oomen et al. 2020). Tightly linked polygenic architectures, such as inversions, resemble single large-effect loci and underlie diverse traits under selection. My research group incorporates experimental data and genomic architectures into mathematical models to forecast population dynamics and trait evolution in marine species under environmental change. These forecasts support evidence-based decision making in environmental policy. Their development will also reveal fundamental truths about the predictability of ecology and evolution.
Genome sequencing, eco-evolutionary modelling, and genetic simulations are unlocking the potential for genomic forecasts of population, species, and ecosystem responses to environmental change (Oomen & Hutchings 2022). Simulations show that single locus control of a life history trait under harvest-induced selection generates a more variable evolutionary response compared to an unlinked polygenic scenario (Oomen et al. 2020). Tightly linked polygenic architectures, such as inversions, resemble single large-effect loci and underlie diverse traits under selection. My research group incorporates experimental data and genomic architectures into mathematical models to forecast population dynamics and trait evolution in marine species under environmental change. These forecasts support evidence-based decision making in environmental policy. Their development will also reveal fundamental truths about the predictability of ecology and evolution.
Publications**
26 articles published/accepted; 3 preprints/manuscripts in review/revision; h-index = 15
PREPRINTS/MANUSCRIPTS IN REVIEW/REVISIONdoi.org/10.1101/2024.12.02.626363
29) Lozano-Fernandez, J, M Domènech, A Ibos, T Marcussen, TH Struck, RA Oomen, A Böhne, R Monteiro, L Aguilera, M Gut, FC Ferreira, F Cruz, J Gómez-Garrido, TS Alioto, D De Panis [2024]. ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions. bioRxiv. preprint: https://doi.org/10.1101/2024.12.02.626363
28) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings [2022; revision requested]. Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data. bioRxiv. preprint
27) Oomen, RA, E Juliussen, EM Olsen, H Knutsen, S Jentoft, & JA Hutchings [2021; second revision requested]. Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures. bioRxiv. preprint
PEER-REVIEWED
26) Mc Cartney, AM, G Formenti, A Mouton, D De Panis, LS Marins, HG Leitão, ..., RA Oomen, ..., & M Pippel (164 authors) [accepted]. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity. preprint
25) Böhne, A*, R Fernández*, J Leonard*, AM Mc Cartney*, S McTaggart*, J Melo-Ferreira*, R Monteiro*, RA Oomen*, OV Pettersson*, & TH Struck* [accepted]. Contextualising samples: Supporting reference genomes for European biodiversity through sample and sample data collection. npj Biodiversity. preprint *contributed equally
24) Norderhaug, KJ, H Knutsen, K Filbee-Dexter, M Sodeland, PE Jorde, T Wernberg, RA Oomen, & E Moland. 2024. The International Union for Conservation of Nature Red List does not account for intraspecific diversity. ICES Journal of Marine Science, fsae039. doi:10.1093/icesjms/fsae039 LINK
23) Kao, AB, AK Hund, FP Santos, J-G Young, D Bhat, J Garland, RA Oomen, & HF McCreery. 2023. Opposing responses to scarcity emerge from functionally unique sociality drivers. The American Naturalist, 202:302-321. doi:10.1086/725426 LINK / twitter thread
22) Theissinger K, G Formenti, C Fernandes, ..., RA Oomen*, ..., J Höglund (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2023. How genomics can help biodiversity conservation. Trends in Genetics, 39:545-559. doi:10.1016/j.tig.2023.01.005 *middle 21 authors contributed equally LINK
21) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings. 2022. Warming accelerates the onset of the molecular stress response and increases mortality of larval Atlantic cod. Integrative & Comparative Biology, 62:1784–1801. doi:10.1093/icb/icac145 LINK
20) Oomen, RA & JA Hutchings. 2022. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. Journal of Animal Ecology, 91:1073-1087. doi:10.1111/1365-2656.13707 Invited LINK / twitter thread / podcast
19) Rasmussen JH, M Moyano, L Fuiman, & RA Oomen. 2022. FishSizer: Software solution for efficiently measuring larval fish size. Ecology & Evolution, 12:e8672. doi:10.1002/ece3.8672 LINK / twitter thread
18) Goodwin M*, KT Halvorsen*, L Jiao*, KM Knausgård*, AH Martin*, M Moyano*, RA Oomen*^, JH Rasmussen*, TK Sørdalen*, & SH Thorbjørnsen*. 2022. Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook. ICES Journal of Marine Science, 79:319–336. doi:10.1093/icesjms/fsab255 *all authors contributed equally ^corresponding author LINK / twitter thread
17) Formenti, G, K Theissinger, C Fernandes, ..., RA Oomen*, ..., M Bálint (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37:197-202. doi:10.1016/j.tree.2021.11.008 *middle 21 authors contributed equally LINK
16) Wolf, JF, L MacKay*, SE Haworth*, ML Cossette*, MN Dedato*, KB Young*, CI Elliott*, & RA Oomen. 2021. Preprinting is positively associated with early career researcher status in ecology and evolution. Ecology & Evolution, 11:13624-13632. doi:10.1002/ece3.8106 *contributed equally LINK / twitter thread / podcast
15) Raatikainen, KJ, J Purhonen, T Pohjanmies, M Peura, …, RA Oomen*, …, J Ziemacki* (31 authors). 2021. Pathways towards a sustainable future envisioned by early-career conservation researchers. Conservation Science & Practice, 3:e493. doi:10.1111/csp2.493 *last 24 authors contributed equally LINK
14) Deininger, A, AH Martin, JC Pardo, PR Berg*, J Bhardwaj*, D Catarino*, A Fernandez-Chacon*, K Martinez-Swatson*, K Ono*, RA Oomen*, M Sodeland*, TK Sørdalen*, A-E Synnes*, SH Thorbjørnsen*, & J Thormar*. 2021. Coastal research seen through an early career lens – a perspective on barriers to interdisciplinarity in Norway. Frontiers in Marine Science, 8:634999. doi:10.3389/fmars.2021.634999 *contributed equally LINK
13) Oomen, RA & JA Hutchings. “Evolution of Reaction Norms.” In Oxford Bibliographies in Evolutionary Biology. Ed. D Futuyma. New York: Oxford University Press, October 28, 2020. doi:10.1093/OBO/9780199941728-0130 Commission LINK / twitter thread
12) Oomen, RA, A Kuparinen, & JA Hutchings. 2020. Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change. Journal of Heredity, 111:319-332. doi:10.1093/jhered/esaa020 Invited & Editor's Choice PDF / twitter thread / presentation / podcast
11) Mérot, C*, RA Oomen*, A Tigano*, & M Wellenreuther*. 2020. A roadmap for understanding the evolutionary significance of structural genomic variation. Trends in Ecology and Evolution, 35:561-572. doi:10.1016/j.tree.2020.03.002 *all authors contributed equally Featured article PDF / twitter thread
10) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2018. Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish. Ecology & Evolution, 8:11634-11644. doi:10.1002/ece3.4615 PDF
9) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2017. Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish. ICES Journal of Marine Science, 75:1353-1361. doi:10.1093/icesjms/fsx232 PDF
8) Oomen, RA & JA Hutchings. 2017. Transcriptomic responses to environmental change in fishes: insights from RNA-seq. FACETS, 2:610–641. doi:10.1139/facets-2017-0015 PDF / popular science article
7) Oomen, RA & JA Hutchings. 2016. Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. Canadian Journal of Zoology, 94:257-264. doi:10.1139/cjz-2015-0186 PDF
6) Kuparinen, A, NE Roney, RA Oomen, JA Hutchings, & EM Olsen. 2015. Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units. ICES Journal of Marine Science, 73:286-292. doi:10.1093/icesjms/fsv181 PDF
5) Oomen, RA & JA Hutchings. 2015. Genetic variability in reaction norms in fishes. Environmental Reviews, 23:353-366. doi:10.1139/er-2014-0077 PDF
4) Oomen, RA & JA Hutchings. 2015. Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conservation Physiology, 3:1-12. doi:10.1093/conphys/cov027 PDF
PREPRINTS/MANUSCRIPTS IN REVIEW/REVISIONdoi.org/10.1101/2024.12.02.626363
29) Lozano-Fernandez, J, M Domènech, A Ibos, T Marcussen, TH Struck, RA Oomen, A Böhne, R Monteiro, L Aguilera, M Gut, FC Ferreira, F Cruz, J Gómez-Garrido, TS Alioto, D De Panis [2024]. ERGA-BGE Reference Genome of Gluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions. bioRxiv. preprint: https://doi.org/10.1101/2024.12.02.626363
28) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings [2022; revision requested]. Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data. bioRxiv. preprint
27) Oomen, RA, E Juliussen, EM Olsen, H Knutsen, S Jentoft, & JA Hutchings [2021; second revision requested]. Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures. bioRxiv. preprint
PEER-REVIEWED
26) Mc Cartney, AM, G Formenti, A Mouton, D De Panis, LS Marins, HG Leitão, ..., RA Oomen, ..., & M Pippel (164 authors) [accepted]. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity. preprint
25) Böhne, A*, R Fernández*, J Leonard*, AM Mc Cartney*, S McTaggart*, J Melo-Ferreira*, R Monteiro*, RA Oomen*, OV Pettersson*, & TH Struck* [accepted]. Contextualising samples: Supporting reference genomes for European biodiversity through sample and sample data collection. npj Biodiversity. preprint *contributed equally
24) Norderhaug, KJ, H Knutsen, K Filbee-Dexter, M Sodeland, PE Jorde, T Wernberg, RA Oomen, & E Moland. 2024. The International Union for Conservation of Nature Red List does not account for intraspecific diversity. ICES Journal of Marine Science, fsae039. doi:10.1093/icesjms/fsae039 LINK
23) Kao, AB, AK Hund, FP Santos, J-G Young, D Bhat, J Garland, RA Oomen, & HF McCreery. 2023. Opposing responses to scarcity emerge from functionally unique sociality drivers. The American Naturalist, 202:302-321. doi:10.1086/725426 LINK / twitter thread
22) Theissinger K, G Formenti, C Fernandes, ..., RA Oomen*, ..., J Höglund (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2023. How genomics can help biodiversity conservation. Trends in Genetics, 39:545-559. doi:10.1016/j.tig.2023.01.005 *middle 21 authors contributed equally LINK
21) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings. 2022. Warming accelerates the onset of the molecular stress response and increases mortality of larval Atlantic cod. Integrative & Comparative Biology, 62:1784–1801. doi:10.1093/icb/icac145 LINK
20) Oomen, RA & JA Hutchings. 2022. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. Journal of Animal Ecology, 91:1073-1087. doi:10.1111/1365-2656.13707 Invited LINK / twitter thread / podcast
19) Rasmussen JH, M Moyano, L Fuiman, & RA Oomen. 2022. FishSizer: Software solution for efficiently measuring larval fish size. Ecology & Evolution, 12:e8672. doi:10.1002/ece3.8672 LINK / twitter thread
18) Goodwin M*, KT Halvorsen*, L Jiao*, KM Knausgård*, AH Martin*, M Moyano*, RA Oomen*^, JH Rasmussen*, TK Sørdalen*, & SH Thorbjørnsen*. 2022. Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook. ICES Journal of Marine Science, 79:319–336. doi:10.1093/icesjms/fsab255 *all authors contributed equally ^corresponding author LINK / twitter thread
17) Formenti, G, K Theissinger, C Fernandes, ..., RA Oomen*, ..., M Bálint (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37:197-202. doi:10.1016/j.tree.2021.11.008 *middle 21 authors contributed equally LINK
16) Wolf, JF, L MacKay*, SE Haworth*, ML Cossette*, MN Dedato*, KB Young*, CI Elliott*, & RA Oomen. 2021. Preprinting is positively associated with early career researcher status in ecology and evolution. Ecology & Evolution, 11:13624-13632. doi:10.1002/ece3.8106 *contributed equally LINK / twitter thread / podcast
15) Raatikainen, KJ, J Purhonen, T Pohjanmies, M Peura, …, RA Oomen*, …, J Ziemacki* (31 authors). 2021. Pathways towards a sustainable future envisioned by early-career conservation researchers. Conservation Science & Practice, 3:e493. doi:10.1111/csp2.493 *last 24 authors contributed equally LINK
14) Deininger, A, AH Martin, JC Pardo, PR Berg*, J Bhardwaj*, D Catarino*, A Fernandez-Chacon*, K Martinez-Swatson*, K Ono*, RA Oomen*, M Sodeland*, TK Sørdalen*, A-E Synnes*, SH Thorbjørnsen*, & J Thormar*. 2021. Coastal research seen through an early career lens – a perspective on barriers to interdisciplinarity in Norway. Frontiers in Marine Science, 8:634999. doi:10.3389/fmars.2021.634999 *contributed equally LINK
13) Oomen, RA & JA Hutchings. “Evolution of Reaction Norms.” In Oxford Bibliographies in Evolutionary Biology. Ed. D Futuyma. New York: Oxford University Press, October 28, 2020. doi:10.1093/OBO/9780199941728-0130 Commission LINK / twitter thread
12) Oomen, RA, A Kuparinen, & JA Hutchings. 2020. Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change. Journal of Heredity, 111:319-332. doi:10.1093/jhered/esaa020 Invited & Editor's Choice PDF / twitter thread / presentation / podcast
11) Mérot, C*, RA Oomen*, A Tigano*, & M Wellenreuther*. 2020. A roadmap for understanding the evolutionary significance of structural genomic variation. Trends in Ecology and Evolution, 35:561-572. doi:10.1016/j.tree.2020.03.002 *all authors contributed equally Featured article PDF / twitter thread
10) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2018. Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish. Ecology & Evolution, 8:11634-11644. doi:10.1002/ece3.4615 PDF
9) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2017. Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish. ICES Journal of Marine Science, 75:1353-1361. doi:10.1093/icesjms/fsx232 PDF
8) Oomen, RA & JA Hutchings. 2017. Transcriptomic responses to environmental change in fishes: insights from RNA-seq. FACETS, 2:610–641. doi:10.1139/facets-2017-0015 PDF / popular science article
7) Oomen, RA & JA Hutchings. 2016. Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. Canadian Journal of Zoology, 94:257-264. doi:10.1139/cjz-2015-0186 PDF
6) Kuparinen, A, NE Roney, RA Oomen, JA Hutchings, & EM Olsen. 2015. Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units. ICES Journal of Marine Science, 73:286-292. doi:10.1093/icesjms/fsv181 PDF
5) Oomen, RA & JA Hutchings. 2015. Genetic variability in reaction norms in fishes. Environmental Reviews, 23:353-366. doi:10.1139/er-2014-0077 PDF
4) Oomen, RA & JA Hutchings. 2015. Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conservation Physiology, 3:1-12. doi:10.1093/conphys/cov027 PDF
3) Oomen, RA, RM Gillett, & CJ Kyle. 2013. Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage. Molecular Ecology Resources, 13:103-116. doi:10.1111/1755-0998.12027 PDF
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2) Oomen, RA, MW Reudink, JJ Nocera, CM Somers, MC Green, & CJ Kyle. 2011. Mitochondrial evidence for panmixia despite perceived barriers to gene flow in a widely distributed waterbird. Journal of Heredity, 102:584-592. doi:10.1093/jhered/esr055 Journal cover image PDF
1) Reudink, MW, CJ Kyle, JJ Nocera, RA Oomen, MC Green, & CM Somers. 2011. Panmixia on a continental scale in a widely distributed colonial waterbird. Biological Journal of the Linnean Society, 102:583-592. doi:10.1111/j.1095-8312.2010.01608.x PDF |
Journal of Heredity cover image; Photo credit: Scott Butner
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All photos are mine unless otherwise specified. This site is optimized for desktop/tablet, so strange things can happen on a mobile/tablet.