Paper repository

Michael Matschiner

Peer-reviewed papers

Roth et al. 2020

Roth O, Solbakken MH, Tørresen OK, Bayer T, Matschiner M, Baalsrud H, Hoff SNK, Brieuc MSO, Haase D, Hanel R, Reusch TBH, Jentoft S (2020) Evolution of male pregnancy associated with remodeling of canonical vertebrate immunity in seahorses and pipefishes. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1916251117. pdf.

Barth et al. 2020

Barth JMI, Gubili C, Matschiner M (shared first co-author), Tørresen OK, Watanabe S, Egger B, Han Y-S, Feunteun E, Sommaruga R, Jehle R, Schabetsberger R (2020) Stable species boundaries despite ten million years of hybridization in tropical eels. Nature Communications, 11:1433. pdf.

Fang et al. 2020

Fang B, Merilä, Matschiner M, Momigliano P (2020) Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent. Molecular Phylogenetics and Evolution, 142:106646. pdf.

Varadharajan et al. 2019

Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J (2019) A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome. Genome Biology and Evolution, 11:3291-3308. pdf.

Matschiner 2019

Matschiner M (2019) Selective sampling of species and fossils influences age estimates under the fossilized birth-death model. Frontiers in Genetics, doi:10.3389/fgene.2019.01064. pdf.

Musilova et al. 2019

Musilova Z, Cortesi F, Matschiner M, Davies WIL, Patel JS, Stieb SM, de Busserolles F, Malmstrøm M, Tørresen OK, Brown CJ, Mountford JK, Hanel R, Stenkamp DL, Jakobsen KS, Carleton KL, Jentoft S, Marshall J, Salzburger W (2019) Vision using multiple distinct rod opsins in deep-sea fishes. Science, 364:588-592. pdf.

Bouckaert et al. 2019

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, de Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie H, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu C-H, Xie W, Zhang C, Stadler T, Drummond AJ (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Computational Biology, 15:e1006650. pdf.

Ceballos et al. 2019

Ceballos SG, Roesti M, Matschiner M, Fernández D, Damerau M, Hanel R, Salzburger W (2019) Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries. BMC Evolutionary Biology, 19:13. pdf.

Matschiner 2019

Matschiner M (2019) Gondwanan vicariance or trans-Atlantic dispersal of cichlid fishes: a review of the molecular evidence. Hydrobiologia, 832:9-37. pdf.

Langangen et al. 2019

Langangen Ø, Färber L, Stige LC, Diekert FK, Barth JMI, Matschiner M, Berg PR, Star B, Stenseth NC, Jentoft S, Durant JM (2019) Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod. Global Change Biology, 25:134-143. pdf.

Malmstrom et al. 2018

Malmstrøm M, Britz R, Matschiner M, Tørresen OK, Hadiaty RK, Yaakob N, Tan YH, Jakobsen KS, Salzburger W, Rüber L (2018) The most developmentally truncated fishes show extensive Hox gene loss and miniaturized genomes. Genome Biology and Evolution, 10:1088-1103. pdf.

Stange et al. 2018

Stange M, Sánchez-Villagra MR, Salzburger W, Matschiner M (2018) Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian Isthmus. Systematic Biology, 67:681-699. pdf.

Runemark et al. 2018

Runemark A, Trier CN, Eroukhmanoff F, Hermansen JS, Matschiner M, Ravinet M, Elgvin TO, Saetre GP (2018) Variation and constraints in hybrid genome formation. Nature Ecology and Evolution, 2:549-556. pdf.

Toljagic et al. 2018

Toljagić O, Voje KL, Matschiner M, Liow LH, Hansen T (2018) Millions of years behind: slow adaptation of ruminants to grasslands. Systematic Biology, 67:145-157. pdf.

Baalsrud et al. 2017

Baalsrud HT, Voje KL, Tørresen OK, Solbakken MH, Matschiner M, Malmstrøm M, Hanel R, Salzburger W, Jakobsen KS, Jentoft S (2017) Evolution of hemoglobin genes in codfishes influenced by ocean depth. Scientific Reports, 7:7956. pdf.

Meyer et al. 2017

Meyer BS, Matschiner M (shared first co-author), Salzburger W (2017) Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes. Systematic Biology, 66:531-550. pdf.

Barth et al. 2017

Barth JMI, Damerau M, Matschiner M, Jentoft S, Hanel R (2017) Genomic differentiation and demographic histories of Atlantic and Indo-Pacific yellowfin tuna (Thunnus albacares) populations. Genome Biology and Evolution, 9:1084-1098. pdf.

Matschiner et al. 2017

Matschiner M, Musilová Z, Barth JMI, Starostová Z, Salzburger W, Steel M, Bouckaert R (2017) Bayesian phylogenetic estimation of clade ages supports trans-Atlantic dispersal of cichlid fishes. Systematic Biology, 66:3-22. pdf.

Malmstrom et al. 2017

Malmstrøm M, Matschiner M, Tørresen OK, Jakobsen KS, Jentoft S (2017) Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Scientific Data, 4:160132. pdf.

Gante et al 2016

Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W (2016) Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Molecular Ecology, 25:6143-6161. pdf.

Malmstrom et al. 2016

Malmstrøm M, Matschiner M (shared first co-author), Tørresen OK, Star B, Snipen LG, Hansen TF, Baalsrud HT, Nederbragt AJ, Hanel R, Salzburger W, Stenseth NC, Jakobsen KS, Jentoft S (2016) Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics, 48:1204-1210. pdf.

Matschiner 2016

Matschiner M (2016) Fitchi: haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics, 32:1250-1252. pdf.

Colombo et al. 2015

Colombo M, Damerau M, Hanel R, Salzburger W, Matschiner M (2015) Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes. Journal of Evolutionary Biology, 28:376-394. pdf.

Meyer et al. 2015

Meyer BS, Matschiner M, Salzburger W (2015) A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Molecular Phylogenetics and Evolution, 83:56-71. pdf.

Damerau et al. 2014

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. pdf.

Barth et al. 2013

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

Damerau et al. 2012

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. pdf.

Palandacic et al. 2012

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

Rutschmann et al. 2011

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. pdf.

Matschiner et al. 2011

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

Matschiner et al. 2009

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

Matschiner & Salzburger 2009

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


Malinsky et al. 2020

Malinsky M, Matschiner M, Svardal H (2020) Dsuite - fast D-statistics and related admixture evidence from VCF files. bioRxiv, doi:10.1101/634477. pdf.

Book chapters

Matschiner et al. 2015

Matschiner M, Colombo M, Damerau M, Ceballos S, Hanel R, Salzburger W (2015) The adaptive radiation of notothenioid fishes in the waters of Antarctica. In: Extremophile Fishes (eds Riesch R, Tobler M, Plath M), pp. 35-57. Springer International Publishing, Switzerland. pdf.

Matschiner et al. 2010

Matschiner M, Hanel R, Salzburger W (2010) Phylogeography and speciation processes in marine fishes and fishes from large freshwater lakes. In: Phylogeography: Concepts, Intraspecific Patterns and Speciation Processes (ed Rutgers DS), pp. 1-29. Nova Science Publishers, New York. pdf.


Musilova et al. 2019

Matschiner M, Salzburger W (2019) Evolution: Genomic signatures of mimicry and mimicry of genomic signatures. Current Biology, 29:R363-R365. pdf.


Sands et al. 2012

Sands C, Arntz W, Janussen D, Agrawal S, Damerau M, Hauquier F, Havermans C, Hirse T, Matschiner M, Knust R, Koschnick N, Mintenbeck K, Montiel A, Rath L, Robert H, Rose A, Rossi S, Storch D, Uriz I, Wang C (2012) Biodiversity, biogeography, phylogeography and phylogenetics in a latitudinal cline. Reports on Polar and Marine Research 644: 13-46. pdf.

Publications discussing my work

Pennisi 2018

Pennisi E (2019) In the deep, dark, ocean fish have evolved superpowered vision. Science, doi:10.1126/science.aax9834.

McGrath 2018

McGrath C (2018) Highlight: Big surprises from the world's smallest fish. Genome Biology and Evolution 10:1104-1105. pdf.

Parham 2016

Parham P (2016) News and Views: How the codfish changed its immune system. Nature Genetics 48:1103-1104. pdf.

Ingram & Mahler 2011

Ingram T, Mahler DL (2011) Perspective: Niche diversification follows key innovation in Antarctic fish radiation. Molecular Ecology 20:4590-4591. pdf.