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Peer-reviewed publications:

  1. Sommer-Trembo, C., Santos, M. E., Clark, B., Werner, M., Fages, A., Matschiner, M., Hornung, S., Ronco, F., Oliver, C., Garcia, C., Tschopp, P., Malinsky, M.* & Salzburger, W.* (2024) The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes. Science 384, 470–475. doi: https://doi.org/10.1126/science.adj9228. *joint corresponding authors

  2. Koppetsch, T., Malinsky, M., Matschiner, M. (2024) Towards reliable detection of introgression in the presence of among-species rate variation. Systematic Biology, syae028; doi: https://doi.org/10.1093/sysbio/syae028. 

  3. Choo, L.Q., Spagliardi, G., Malinsky, M., Choquet, M., Goetze, E., Hoarau, G. and Peijnenburg, K.T.C.A. (2023), Genome-wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides. Molecular Ecology. 32, 3200–3219. doi: https://doi.org/10.1111/mec.16931.

  4. Barth, J.M.I., Handley, S.A., Kintzl, D., Leonard, G., Malinsky, M., Matschiner, M., Meyer, B. S., Salzburger, W., Stefka, J., Trucchi, E. (2023) The history and organization of the Workshop on Population and Speciation Genomics. Evolution: Education & Outreach 16, 2. doi: https://doi.org/10.1186/s12052-023-00182-w.

  5. Vernaz, G., Hudson, A. G., Santos, M. E., Fischer, B., Carruthers, M., Shechonge, A. H., Gabagambi, N. P., Tyers, A. M., Ngatunga, B. P., Malinsky, M., Durbin, R., Turner, G. F., Genner, M. J. & Miska, E. A. (2022) Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish. Nature Ecology & Evolution, 1-12. doi: https://doi.org/10.1038/s41559-022-01894-w.

  6. Vernaz, G., Malinsky, M, Svardal, H., Du, M., Tyers, A. M., Santos, M. E., Durbin, R., Genner, M. J., Turner, G. F. & Miska, E. A. (2021) Mapping Epigenetic Divergence in the Massive Radiation of Lake Malawi Cichlid Fishes. Nature Communications 12, 5870. doi: https://doi.org/10.1038/s41467-021-26166-2.

  7. Rhie, A., McCarthy, S. A. ... (44 others) ... Malinsky, M., ... (72 others) ... Durbin, R., Phillippy, A. M. & Jarvis, E. D. (2021) Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746. doi: https://doi.org/10.1038/s41586-021-03451-0.

  8. Svardal, H., Salzburger, W. & Malinsky, M. (2021) Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes. Annu Rev Anim Biosci 9 (1), 55–79. doi: https://doi.org/10.1146/annurev-animal-061220-023129.

  9. Malinsky, M., Matschiner, M. & Svardal, H. (2021) Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files. Molecular Ecology Resources 21 (2), 584-595. doi: https://doi.org/10.1111/1755-0998.13265.

  10. Ronco, F., Matschiner, M., Böhne, A., Boila, A., Büscher, H.H., El Taher, A., Indermaur, A., Malinsky, M., Ricci, V., Kahmen, A., Jentoft, S. & Salzburger, W. (2021) Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature 589, 76-81. doi: https://doi.org/10.1038/s41586-020-2930-4.

  11. Ciezarek, A., Ford, AGP., Etherington, G.J., Kasozic, N., Malinsky, M., Mehta, T., Penso-Dolfine, L., Ngatunga, B.P., Shechonge, A., Tamatamah, R., Haerty, W., Di Palma, F., Genner, M.J. & Turner, G.F. (2021) Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes. Aquaculture, 737637. doi: https://doi.org/10.1016/j.aquaculture.2021.737637.

  12. Patil, C., Sylvester, J. B., Abdilleh, K., Norsworthy, M. W., Pottin, K., Malinsky, M., Bloomquist, R. F., Johnson, Z. V., McGrath, P. T. & Streelman, J. T. (2021) Genome-enabled inference of evolutionary divergence in brains and behavior. Scientific Reports. doi: https://doi.org/10.1101/2020.10.12.336453.

  13. Carleton, K. L., Conte, M. A., Malinsky, M., Nandamuri, S. P., Sandkam, B. A., Meier, J. I., Mwaiko, S., Seehausen, O. & Kocher, T. D. (2020) Movement of transposable elements contributes to cichlid diversity. Molecular Ecology. doi: https://doi.org/10.1111/mec.15685.

  14. Svardal, H., Quah, F. X., Malinsky, M., Ngatunga, B. P., Miska, E. A., Salzburger, W., Genner, M. J., Turner, G. F. & Durbin, R. (2020) Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation. Molecular Biology and Evolution 37, 1100–1113.

  15. Malinsky, M., Svardal, H., Tyers, A. M., Genner, M. J., Turner, G. F. Miska, E. A., Durbin, R. (2018) Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature Ecology & Evolution 2, 1940–1955. doi: https://doi.org/10.1038/s41559-018-0717-x
    (also see Nat. Ecol. Evo. "Behind the paper" story)

  16. Malinsky, M., Trucchi, E., Lawson, D. J. & Falush, D. (2018) RADpainter and fineRADstructure: Population Inference from RADseq Data. Molecular Biology and Evolution 35, 1284–1290. doi: https://doi.org/10.1093/molbev/msy023.

  17. Malinsky, M. & Salzburger, W. (2016) Environmental context for understanding the iconic adaptive radiation of cichlid fishes in Lake Malawi. PNAS 113, 11654–11656. doi: https://doi.org/10.1073/pnas.1614272113.

  18. Malinsky, M., Challis, R., Tyers, A. M., Schiffels, S., Terai, Y., Ngatunga, B. P., Miska, E. A., Durbin, R., Genner, M. J., Turner, G. F.  (2015) Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science (New York, N.Y.) 350, 1493–1498. doi: https://doi.org/10.1126/science.aac9927.

  19. Brawand, D., Wagner, C. E., Li, Y. I., Malinsky, M., Keller, I., … (81 others) … and Di Palma, F. (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513(7518), 375–381. doi: https://doi.org/10.1038/nature13726.

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Preprints:

  1. Talbi, M., Turner, G. F & Malinsky, M. (2024) Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko. bioRxiv 2024.03.20.585960; doi: https://doi.org/10.1101/2024.03.20.585960.

  2. Nichols, A. L. A., Shafer, M. E. R, Indermaur, A., Rüegg, A., Gonzalez-Dominguez, R., Malinsky, M., Sommer-Trembo, C., Fritschi, L., Salzburger, W. & Schier, A. F. (2024) Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes. bioRxiv 2024.05.29.596472, doi: https://doi.org/10.1101/2024.05.29.596472.

  3. Omelchenko, D., Bitja-Nyom, A. R., Matschiner, M., Malinsky, M., Indermaur, A., Salzburger, W., Bartoš, O. & Musilova, Z. (2024) Hemoglobin gene repertoire in teleost and cichlid fishes shaped by gene duplications and genome rearrangements. bioRxiv 2024.03.26.586788; doi: https://doi.org/10.1101/2024.03.26.586788.

  4. Blumer, L. M., Burskaia, V., Artiushin, I., Saha, J., Camacho Garcia, J., Elkin, J., Fischer, B., Zhou, C., Gresham, S., Malinsky, M., Linderoth, T. ... (14 others) ..., Turner, G.F., Durbin, R. & Savrdal, H. (2024) Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation. bioRxiv 2024.07.28.605452; doi: https://doi.org/10.1101/2024.07.28.605452.

  5. Malinsky, M., Simpson, J. T. & Durbin, R. (2016) trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios. bioRxiv. doi: https://doi.org/10.1101/051516.

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PUBLICATIONS

References and Links to Papers - see also Google Scholar

preprint assemblies
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