Asterisk (*) denotes shared first authorship and cross (†) denotes supervised student
Manuscripts in preparation/revision 26. Singh P, Tschanz-Lischer H, Ahi EP, Ford K, Mwaiko S, Haesler M, Marques D, Bruggman R and Seehausen O. Multifarious selection and polygenic architectures underlies speciation and adaptive radiation. In preparation. 25. Singh P, Duenser A†, Ahi EP, Durdevic M, Gessl W, Schaeffer S, Seehausen O and Sturmbauer C. Evolutionary dynamics of alternative splicing and gene expression underlying dietary transitions during adaptive radiation. In preparation. 24. Ahi EP & Singh P. An emerging orchestrator of eco-evolutionary adaptation: m6A regulation of post-transcriptional mechanisms. In revision. 23. Duenser A*†, Singh P*, Ahi EP, Durdevic M, Gessl W, Schaeffer S, Seehausen O and Sturmbauer C. Developmental dynamics of alternative splicing and gene expression during rapid adaptive radiation. In Revision. BioRXiv: doi: https://doi.org/10.1101/2024.01.24.577063 Published 2024 22. Ahi EP, Verta J, Kurko J, Ruokolainen A, Singh P, Debes PV, Erkinaro J, and Primmer C. Gene co-expression patterns in Atlantic Salmon adipose tissue provide a molecular link among seasonal changes, energy balance and age at maturity. Molecular Ecology doi: 10.1101/2023.08.30.555548. 21. Whiting J, Booker T, Rougeux C, Lind B, Singh P et al. Core genes driving climate adaptation in plants. Accepted Nature Ecology & Evolution. 20. Peñalba JV, Runemark A, Meier J, Singh P, Wogan G, Sánchez-Guillén, R, Mallet J, Rometsch SJ, Menon M, Seehausen O, Kulmuni J, Pereira RJ. The role of hybridisation in species formation and persistence. Cold Spring Harbour Perspectives in Biology. 2024.cshperspectives.cshlp.org/content/early/2024/03/01/cshperspect.a041445.abstract#:~:text=Hybridization%20is%20a%20multifaceted%20evolutionary,require%20cooperation%20among%20different%20subdisciplines. 19. Lind BM, Candido-Ribeiro R, Singh P, Lu M, Vidakovic DO, Booker TR, Whitlock MC, Yeaman S, Isabel N, Aitken SN. How useful is genomic data for predicting maladaptation to future climate? Global Change Biology. 2024. 18. Singh P, StClair B, Lind BM, Cronn R, Wilhelmi NP, Lu M, Vidakovic DO, Hamelin R, Shaw D, Aitken S and Yeaman S. Genetic architecture of resistance and tolerance to Swiss needle cast and Rhabdocline needle cast diseases in Douglas-fir. In press New Phytologist EcoEvoRxiv. doi: 10.32942/osf.io/s5rd7 2023 17. Duenser, A. †, Singh, P., Lecaudey, L.A., Sturmbauer, C., Albertson, C., Gessl, W., Ahi, E.P., 2022. Conserved molecular players involved in human nose morphogenesis underlie evolutionary of the exaggerated snout phenotype in cichlids. Genome Biology and Evolution. 2023. https://doi.org/10.1093/gbe/evad045 16. Singh P, Taborsky M, Peichel CL, and Sturmbauer C. Genomic basis of Y-linked dwarfism in a shell-brooding cichlid. Molecular Ecology, 2023. doi: https://doi.org/10.1111/mec.16839 See Molecular Ecology Spotlight of our article: https://molecularecologyblog.com/tag/sex-chromosomes/ Paper was picked for Faculty Opinions: https://connect.h1.co/article/742477180?_gl=1*r78h7o*_up*MQ..*_ga*NTExODE3NS4xNjc0NjYzNDEx*_ga_H9GENGJ8TW*MTY3NDY2MzQxMC4xLjAuMTY3NDY2MzQxMC4wLjAuMA 2022 15. Singh P, Irisarri I, Torres-Dowdall J, Thallinger GG, Svardal H, Lemmon AR, Lemmon EM, Koblmüller S, Meyer A and Sturmbauer C. 2022. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and suggests repeated parallelism of eco-morphologies. Ecology and Evolution. 17;12(7):e9077. doi: https://doi.org/10.1002/ece3.9077 14. Jasper R, McDonald TK, Singh P, Lu M, Rougeux C, Lind B, Yeaman S. Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch. Molecular Ecology Resources, 2022. doi: https://doi.org/10.1111/1755-0998.13628 13. Singh P and Ahi EP. The importance of alternative splicing in adaptive evolution. Molecular Ecology, 2022. doi:https://doi.org/10.1111/mec.16377 pre-2022 12. Lind BM, Lu M, Vidakovic DO, Singh P, Booker TR, Aitken SN and Yeaman S. 2021. Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species. Molecular Ecology Resources, 2021, 22, 225–238. doi.org/https://doi.org/10.1111/1755-0998.13474 11. Lecaudey LA, Singh P, Sturmbauer S, Duenser A, Gessl W, and Ahi EP. Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris. BMC Genomics, 2021, 22:506 10. Singh P, Ahi EP, and Sturmbauer C. Gene co-expression networks reveal molecular interactions underlying cichlid jaw modularity. 2021. BMC Evolutionary Biology, 21:62 9. Qiushi L, Ramasamy S, Singh P, Hagel JM, Dunemann S, Chen X, Chen R, Lisa Yu, Joseph Tucker JE, Facchini PJ & Yeaman S. 2020. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy. Nature Communications, 11 (1), 1-13 8. Ahi EP, Duenser A†, Singh P, Gessl W, and Stumbauer S. 2020. Appetite regulating genes may contribute to herbivory versus carnivory divergence in haplochromine cichlids. PeerJ, 8, e8375 7. Lecaudey LA, Sturmbauer S, Singh P, and Ahi EP. 2019. Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii. Scientific Reports, 9-20296 6. Ahi EP, Singh P, Duenser A†, Gessl W, and Sturmbauer S. 2019. Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging. BMC Evolutionary Biology, 19:150 5. Ahi EP, Singh P, Lecaudey LA, Gessl W, and Sturmbauer S. 2018. Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization. Evodevo, 9:1–17. 4. Irissari I*, Singh P*, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon AR, Lemmon EM, Thallinger GG, Sturmbauer C and Meyer A. 2018. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika. Nature Communications, 9(3159) 3. Singh P, Börger C, More H, and Sturmbauer C. 2017. The role of alternative splicing and differential gene expression in cichlid adaptive radiation. Genome Biology and Evolution, 9 (10), 2764–2781 2. Abila R, Akoll P, Albertson C, Antunes D, Banda T, Bills R, Bulirani A, Chocha Manda A, Cohen A, Cunha-Saraiva F, Derycke S, Donohue I, Du M, Dudu A, Egger B, Fritzsche K, Frommen J, Gante H, Genner M, Härer A, Hata H, Irvine K, Isumbisho Mwapu P, Janssens de Bisthoven L, Jungwirth A, Kaleme P, Katongo C, Kéver L, Koblmüller S, Konings A, Lamboj A, Lemmel-Schaedelin F, Machado Schiaffino G, Martens K, Masilya Mulungula P, Meyer A, More H, Musilová Z, Muterezi Bukinga F, Muzumani D, Ntakimazi G, Okello W, Phiri H, Piálek L, Plisnier P, Raeymaekers J, Rajkov J, Říčan O, Roberts R, Salzburger W, Schoen I, Sefc K, Singh P et al. 2016. Oil extraction imperils Africa’s Great Lakes. Science, 354 (6312), 561-562 1. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan ARK, Hussey SG, Pinard D, van der Merwe K, Singh P et al. 2014. The genome of Eucalyptus grandis. Nature, 510, 356-361. |
Behind the paper Singh et al (2023) in Molecular Ecology:
https://go.nature.com/3vzgRiy
This paper also got some media coverage in International, Swiss and Austrian media, which is exciting!
How giants became dwarfs
University of Bern:
www.unibe.ch/news/media_news/media_relations_e/media_releases/2023/media_releases_2023/how_giants_became_dwarfs/index_eng.html
Science Daily:
www.sciencedaily.com/releases/2023/02/230209094126.htm?fbclid=IwAR1LSxtnBiWf9vzZ8caM7qSXFrw6fOQMgYTDGij2DzR95P3lgO0Gx8W5vyk
EurekAlert:
www.eurekalert.org/news-releases/979245?fbclid=IwAR2YX_3EzyaNjDD2DJw9-pyZQXn-2nun7alfRslKaEbel5GhC_hQXVqfOcc
Phys.org:
phys.org/news/2023-02-giants-dwarfs-exploring-size-difference.html
ClimatChange:
www.climatechange.ie/how-giants-became-dwarfs/
Austrian National Public Broadcaster:
steiermark.orf.at/stories/3190067/?fbclid=IwAR0-1Q2OofHtYsER9L9a9cT1AvMYhz_Q6T1BKoqGNugyVnGqUe08M5AcL38
Swiss National Broadcaster:
https://www.srf.ch/audio/wissenschaftsmagazin/wissenschaftsmagazin-themenuebersicht?id=12331129
Press Coverage for Irisarri*, Singh* et al (2018) in Nature Communications: Oldest evidence for diversity boosting hybridization
https://www.eurekalert.org/pub_releases/2018-08/uok-hbe080818.php
https://phys.org/news/2018-08-hybridization-boosts-evolution.html
https://www.uni-konstanz.de/en/university/news-and-media/current-announcements/press-releases/press-releases-in-detail/hybridisierung-als-evolutionsschub/
https://on.uni-graz.at/de/detail/article/artkreuzung-als-evolutions-boost/
https://www.upi.com/Science_News/2018/08/08/African-fish-shows-how-hybridization-drives-evolution/8481533749771/
https://www.breitbart.com/news/african-fish-shows-how-hybridization-drives-evolution/
Behind the paper Irisarri*, Singh* et al (2018) in Nature Communications:
https://natureecoevocommunity.nature.com/users/54859-iker-irisarri/posts/37473-refugees-welcome-anchored-phylogenomics-uncovers-early-hybridization-and-adaptive-loci-shaping-radiation-of-lake-tanganyika-cichlid-fishes
Press coverage for Myburg et al (2014) in Nature: Eucalyptus genome decoded
https://www.sciencedaily.com/releases/2011/05/110512104214.htm
https://www.eurekalert.org/pub_releases/2014-06/osu-gcu060914.php
https://phys.org/news/2014-06-genome-eucalyptus-potential-paper-fuel.html
http://www.dst.gov.za/index.php/media-room/latest-news/955-joint-media-release-decoding-of-eucalyptus-tree-genome-unlocks-new-possibilities-for-renewable-fibre-fuel-and-biomaterials
https://go.nature.com/3vzgRiy
This paper also got some media coverage in International, Swiss and Austrian media, which is exciting!
How giants became dwarfs
University of Bern:
www.unibe.ch/news/media_news/media_relations_e/media_releases/2023/media_releases_2023/how_giants_became_dwarfs/index_eng.html
Science Daily:
www.sciencedaily.com/releases/2023/02/230209094126.htm?fbclid=IwAR1LSxtnBiWf9vzZ8caM7qSXFrw6fOQMgYTDGij2DzR95P3lgO0Gx8W5vyk
EurekAlert:
www.eurekalert.org/news-releases/979245?fbclid=IwAR2YX_3EzyaNjDD2DJw9-pyZQXn-2nun7alfRslKaEbel5GhC_hQXVqfOcc
Phys.org:
phys.org/news/2023-02-giants-dwarfs-exploring-size-difference.html
ClimatChange:
www.climatechange.ie/how-giants-became-dwarfs/
Austrian National Public Broadcaster:
steiermark.orf.at/stories/3190067/?fbclid=IwAR0-1Q2OofHtYsER9L9a9cT1AvMYhz_Q6T1BKoqGNugyVnGqUe08M5AcL38
Swiss National Broadcaster:
https://www.srf.ch/audio/wissenschaftsmagazin/wissenschaftsmagazin-themenuebersicht?id=12331129
Press Coverage for Irisarri*, Singh* et al (2018) in Nature Communications: Oldest evidence for diversity boosting hybridization
https://www.eurekalert.org/pub_releases/2018-08/uok-hbe080818.php
https://phys.org/news/2018-08-hybridization-boosts-evolution.html
https://www.uni-konstanz.de/en/university/news-and-media/current-announcements/press-releases/press-releases-in-detail/hybridisierung-als-evolutionsschub/
https://on.uni-graz.at/de/detail/article/artkreuzung-als-evolutions-boost/
https://www.upi.com/Science_News/2018/08/08/African-fish-shows-how-hybridization-drives-evolution/8481533749771/
https://www.breitbart.com/news/african-fish-shows-how-hybridization-drives-evolution/
Behind the paper Irisarri*, Singh* et al (2018) in Nature Communications:
https://natureecoevocommunity.nature.com/users/54859-iker-irisarri/posts/37473-refugees-welcome-anchored-phylogenomics-uncovers-early-hybridization-and-adaptive-loci-shaping-radiation-of-lake-tanganyika-cichlid-fishes
Press coverage for Myburg et al (2014) in Nature: Eucalyptus genome decoded
https://www.sciencedaily.com/releases/2011/05/110512104214.htm
https://www.eurekalert.org/pub_releases/2014-06/osu-gcu060914.php
https://phys.org/news/2014-06-genome-eucalyptus-potential-paper-fuel.html
http://www.dst.gov.za/index.php/media-room/latest-news/955-joint-media-release-decoding-of-eucalyptus-tree-genome-unlocks-new-possibilities-for-renewable-fibre-fuel-and-biomaterials