Michael Matschiner

Academic Interests

I’m currently working as a bioinformatician in the AquaGenome project. I did my PhD in Basel, Switzerland, on the evolution of Antarctic fishes (Notothenioidei), using phylogenetics and molecular dating to compare the emergence of a particular innovation (antifreeze glycoproteins) with the timing of cooling events in Antarctic waters. We found that both events may have coincided and that the antifreeze glycoproteins may have triggered the adaptive radiation of these fishes.

For my first postdoc I moved to New Zealand, where I collaborated with mathematicians and computer scientists to develop a novel way to time-calibrate phylogenies. I am broadly interested in vertebrate evolution, both over larger time scales and between species, and over short time scales on the population level. I believe that for both macro- and microevolutionary studies we need good estimates of the timing of events, and that these estimates can be obtained with the combination of molecular data, biogeography, and fossils.




Damerau M, Matschiner M, Salzburger W, Hanel R (2014) Population divergences despite long pelagic larval stages: lessons from crocodile icefishes (Channichthyidae). Molecular Ecology, 23:284-299.

Barth JMI, Matschiner M, Robertson BR (2013) Phylogenetic position and subspecies divergence of the endangered New Zealand Dotterel (Charadrius obscurus). PLOS ONE, 8:e78068.

Damerau M, Matschiner M, Salzburger W, Hanel R (2012) Comparative population genetics of seven notothenioid fish species in the southern Scotia Arc, Antarctica. Polar Biology, 35:1073-1086.

Palandaçiç A, Matschiner M, Zupançiç P, Sloj A (2012) Fish migrate underground: the example of Delminichthys adspersus (Cyprinidae). Molecular Ecology, 21:1658-1671.

Rutschmann S, Matschiner M, Damerau M, Muschick M, Lehmann MF, Hanel R, Salzburger W (2011) Parallel ecological diversification in Antarctic notothenioid fishes as evidence for adaptive radiation. Molecular Ecology, 20:4707-4721.

Matschiner M, Hanel R, Salzburger W (2011) On the origin of the notothenioid adaptive radiation. PLoS ONE, 6:e18911.

Matschiner M, Hanel R, Salzburger W (2009) Gene flow by larval dispersal in the Antarctic notothenioid fish Gobionotothen gibberifrons. Molecular Ecology, 18:2574-2587.

Matschiner M, Salzburger W (2009) TANDEM: integrating automated allele binning into genetics and genomics workflows. Bioinformatics, 25:1982-1983.


  • Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2017). Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Scientific Data.  ISSN 2052-4463.  4:160132, s 1- 13 . doi: 10.1038/sdata.2016.132
  • Matschiner, Michael; Musilová, Zuzana; Barth, Julia Maria Isis; Starostová, Zuzana; Salzburger, Walter; Steel, Mike & Bouckaert, Remco (2017). Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes. Systematic Biology.  ISSN 1063-5157.  66(1), s 3- 22 . doi: 10.1093/sysbio/syw076
  • Toljagić, Olja; Voje, Kjetil L.; Matschiner, Michael; Liow, Lee Hsiang & Hansen, Thomas F (2017). Millions of years behind: slow adaptation of ruminants to grasslands.. Systematic Biology.  ISSN 1063-5157. . doi: doi.org/10.1093/sysbio/syx059
  • Gante, Hugo F; Matschiner, Michael; Malmstrøm, Martin; Jakobsen, Kjetill Sigurd; Jentoft, Sissel & Salzburger, Walter (2016). Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Molecular Ecology.  ISSN 0962-1083.  25(24), s 6143- 6161 . doi: 10.1111/mec.13767
  • Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav; Hansen, Thomas F; Baalsrud, Helle Tessand; Nederbragt, Alexander Johan; Hanel, Reinhold; Salzburger, Walter; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics.  ISSN 1061-4036.  48(10), s 1204- 1210 . doi: 10.1038/ng.3645
  • Matschiner, Michael (2016). Fitchi: Haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics.  ISSN 1367-4803.  32(8), s 1250- 1252 . doi: 10.1093/bioinformatics/btv717
  • Meyer, Britta S.; Matschiner, Michael & Salzburger, Walter (2016). Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes. Systematic Biology.  ISSN 1063-5157.  s 1- 20 . doi: 10.1093/sysbio/syw069
  • Colombo, Marco; Damerau, Malte; Hanel, Reinhold; Salzburger, Walter & Matschiner, Michael (2015). Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes. Evolutionary biology.  ISSN 0071-3260.  28, s 376- 394 . doi: 10.1111/jeb.12570
  • Matschiner, Michael; Colombo, Marco; Damerau, Malte; Ceballos, Santiago; Hanel, Reinhold & Salzburger, Walter (2015). The Adaptive Radiation of Notothenioid Fishes in the Waters of Antarctica , In Rüdiger Riesch; Michael Tobler & Martin Plath (ed.),  Extremophile Fishes.  Springer.  ISBN 978-3-319-13362-1.  The Adaptive Radiation of Notothenioid Fishes in the Waters of Antarctica.  s 35 - 57
  • Meyer, Britta S.; Matschiner, Michael & Salzburger, Walter (2015). A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Molecular Phylogenetics and Evolution.  ISSN 1055-7903.  83, s 56- 71 . doi: 10.1016/j.ympev.2014.10.009

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  • Matschiner, Michael; Star, Bastiaan; Barth, Julia Maria Isis; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2017). Genomic rearrangements a phylogenetic approach.
  • Barth, Julia Maria Isis; Star, Bastiaan; Matschiner, Michael; Berg, Paul Ragnar; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2016). Ancient genomic variation separates Atlantic cod ecotypes; implications for management.
  • Matschiner, Michael (2015). Inversions or Introgression: The origin of high-divergence genomic regions in Atlantic cod.
  • Star, Bastiaan; Jentoft, Sissel; Matschiner, Michael; Nederbragt, Alexander Johan; Kjesbu, Olav Sigurd; Berg, Paul Ragnar; Bradbury, Ian R.; Pampoulie, Christophe; Hansen, Marianne Helén Selander; Skage, Morten; Jakobsen, Kjetill Sigurd & Stenseth, Nils Christian (2015). Does historic DNA provide genomic evidence for recent selection in Atlantic cod?.
  • Matschiner, Michael; Star, Bastiaan; Berg, Paul Ragnar; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Hansen, Marianne Helén Selander; Skage, Morten; Kjesbu, Olav Sigurd; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2014). Population differentiation and local adaptation in Atlantic cod.

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Published Oct. 3, 2013 3:45 PM - Last modified Apr. 12, 2014 4:03 PM