Michael Matschiner

• Barth, Julia Maria Isis; Gubili, Chrysoula; Matschiner, Michael; Tørresen, Ole K.; Watanabe, Shun; Egger, Bernd; Han, Yu-San; Feunteun, Eric; Sommaruga, Ruben; Jehle, Robert & Schabetsberger, Robert (2020). Stable species boundaries despite ten million years of hybridization in tropical eels. Nature Communications.  ISSN 2041-1723.  11 . doi: 10.1038/s41467-020-15099-x Full text in Research Archive. Show summary

  Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla) and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past introgression across a time-calibrated phylogeny. We show that the seven species have remained distinct for up to 10 million years and find that the current frequencies of hybridization across species pairs contrast with genomic signatures of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we suggest cytonuclear incompatibilities, hybrid breakdown, and purifying selection as mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of clades.

• Malinsky, M; Matschiner, Michael & Svardal, Hannes (2020). Dsuite - fast D-statistics and related admixture evidence from VCF files. Molecular Ecology Resources.  ISSN 1755-098X.  21(2), s 584- 595 . doi: 10.1111/1755-0998.13265 Show summary

  Patterson's D, also known as the ABBA-BABA statistic, and related statistics such as the f4-ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only small subsets of the available statistics, and are impracti- cal to evaluate all gene flow hypotheses across data sets with many populations or species due to computational inefficiencies. Here, we present a new software pack- age Dsuite, an efficient implementation allowing genome scale calculations of the D and f4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file. Our program also implements statistics suited for application to genomic windows, providing evidence of whether introgression is confined to specific loci, and it can also aid in interpretation of a system of f4-ratio results with the use of the “f-branch” method. Dsuite is available at https://github.com/millanek/Dsuite, is straightforward to use, substantially more computationally efficient than comparable programs, and provides a convenient suite of tools and statistics, including some not previously available in any software package. Thus, Dsuite facilitates the assessment of evidence for gene flow, espe- cially across larger genomic data sets.

• Matschiner, Michael; Böhne, Astrid; Ronco, Fabrizia & Salzburger, Walter (2020). The genomic timeline of cichlid fish diversification across continents. Nature Communications.  ISSN 2041-1723.  11(1) . doi: 10.1038/s41467-020-17827-9 Full text in Research Archive. Show summary

  Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution — the timeline of their diversification — remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.

• Ronco, Fabrizia; Matschiner, Michael; Böhne, Astrid; Boila, Anna; Büscher, Heinz H; El Taher, Athimed; Indermaur, Adrian; Malinsky, Milan; Ricci, Virginie; Kahmen, Ansgar; Jentoft, Sissel & Salzburger, Walter (2020). Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature.  ISSN 0028-0836.  589, s 76- 81 . doi: 10.1038/s41586-020-2930-4 Show summary

  Adaptive radiation is the likely source of much of the ecological and morphological diversity of life1,2,3,4. How adaptive radiations proceed and what determines their extent remains unclear in most cases1,4. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika. On the basis of whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology and lower pharyngeal jaw shape), scoring of pigmentation patterns and approximations of the ecology of nearly all of the approximately 240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of rapid morphospace expansion. We provide empirical support for two theoretical predictions of how adaptive radiations proceed, the ‘early-burst’ scenario1,5 (for body shape) and the stages model1,6,7 (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per-individual heterozygosity, but is not correlated with transposable element content, number of gene duplications or genome-wide levels of selection in coding sequences.

• Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael; Baalsrud, Helle Tessand; Hoff, Siv Nam Khang; Brieuc, Marine Servane Ono; Haase, David Jürgen; Hanel, Reinhold; Reusch, Thorsten B. H. & Jentoft, Sissel (2020). Evolution of male pregnancy associated with remodeling of canonical vertebrate immunity in seahorses and pipefishes. Proceedings of the National Academy of Sciences of the United States of America.  ISSN 0027-8424.  117(17), s 9431- 9439 . doi: 10.1073/pnas.1916251117 Show summary

  A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.

• Bouckaert, Remco; Vaughan, Timothy G; Barrido-Sottani, Joëlle; Duchêne, Sebastián; Fourment, Mathieu; Gavryushkina, Alexandra; Heled, Joseph; Jones, Graham; Kühnert, Denise; De Maio, Nicola; Matschiner, Michael; Mendes, Fábio; Müller, Nicola; Ogilvie, Huw; du Plessis, Louis; Popinga, Alex; Rambaut, Andrew; Rasmussen, David; Siveroni, Igor; Suchard, Marc A.; Wu, Chieh-Hsi; Xie, Dong; Zhang, Chi; Stadler, Tanja & Drummond, Alexei (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology.  ISSN 1553-734X.  15(4) . doi: 10.1371/journal.pcbi.1006650
• Ceballos, Santiago; Roesti, Marius; Matschiner, Michael; Fernandez, Daniel A; Damerau, Malte; Hanel, Reinhold & Salzburger, Walter (2019). Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries. BMC Evolutionary Biology.  ISSN 1471-2148.  19(1), s 1- 14 . doi: 10.1186/s12862-019-1345-z Full text in Research Archive.
• Fang, Bohao; Merilä, Juha; Matschiner, Michael & Momigliano, Paolo (2019). Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent. Molecular Phylogenetics and Evolution.  ISSN 1055-7903.  142, s 1- 5 . doi: 10.1016/j.ympev.2019.106646 Full text in Research Archive. Show summary

  Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, since the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.

• Matschiner, Michael (2019). Gondwanan vicariance or trans-Atlantic dispersal of cichlid fishes: a review of the molecular evidence. Hydrobiologia.  ISSN 0018-8158.  832(1), s 9- 37 . doi: 10.1007/s10750-018-3686-9
• Matschiner, Michael (2019). Selective Sampling of Species and Fossils Influences Age Estimates Under the Fossilized Birth-Death Model. Frontiers in Genetics.  ISSN 1664-8021.  10 . doi: 10.3389/fgene.2019.01064 Full text in Research Archive.
• Musilova, Zuzana; Cortesi, Fabio; Matschiner, Michael; Davies, Wayne I. L.; Patel, Jagdish Suresh; Stieb, Sara M.; De Busserolles, Fanny; Malmstrøm, Martin; Tørresen, Ole K.; Brown, Celeste J.; Mountford, Jessica K.; Hanel, Reinhold; Stenkamp, Deborah L.; Jakobsen, Kjetill Sigurd; Carleton, Karen L.; Jentoft, Sissel; Marshall, Justin & Salzburger, Walter (2019). Vision using multiple distinct rod opsins in deep-sea fishes. Science.  ISSN 0036-8075.  364(6440), s 588- 592 . doi: 10.1126/science.aav4632
• Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F.; Guo, Baocheng; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd & Merilä, Juha (2019). A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biology and Evolution (GBE).  ISSN 1759-6653.  11(11), s 3291- 3308 . doi: 10.1093/gbe/evz240 Full text in Research Archive.
• Runemark, Anna; Trier, Cassandra Nicole; Eroukhmanoff, Fabrice; Hermansen, Jo Skeie; Matschiner, Michael; Ravinet, Mark; Elgvin, Tore Oldeide & Sætre, Glenn-Peter (2018). Variation and constraints in hybrid genome formation. Nature Ecology and Evolution.  ISSN 2397-334X.  2(3), s 549- 556 . doi: 10.1038/s41559-017-0437-7
• Langangen, Øystein; Färber, Leonie Anette; Stige, Leif Christian; Diekert, Florian Klaus; Barth, Julia Maria Isis; Matschiner, Michael; Berg, Paul Ragnar; Star, Bastiaan; Stenseth, Nils Christian; Jentoft, Sissel & Durant, Joel Marcel (2018). 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.  ISSN 1354-1013.  25(1), s 134- 143 . doi: 10.1111/gcb.14474 Full text in Research Archive.
• Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K.; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter & Rüber, Lukas (2018). The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biology and Evolution (GBE).  ISSN 1759-6653.  10(4), s 1088- 1103 . doi: 10.1093/gbe/evy058 Full text in Research Archive.
• Stange, Madlen; Sanchez-Villagra, Marcelo R; Salzburger, Walter & Matschiner, Michael (2018). Bayesian divergence-time estimation with genome-wide single-nucleotide polymorphism data of sea catfishes (Ariidae) supports miocene closure of the Panamanian Isthmus. Systematic Biology.  ISSN 1063-5157.  67(4), s 681- 699 . doi: 10.1093/sysbio/syy006
• Toljagic, Olja; Voje, Kjetil L.; Matschiner, Michael; Liow, Lee Hsiang & Hansen, Thomas F (2018). Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands. Systematic Biology.  ISSN 1063-5157.  67(1), s 145- 157 . doi: 10.1093/sysbio/syx059
• Baalsrud, Helle Tessand; Voje, Kjetil L.; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Matschiner, Michael; Malmstrøm, Martin; Hanel, Reinhold; Salzburger, Walter; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2017). Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Scientific Reports.  ISSN 2045-2322.  7, s 1- 10 . doi: doi:10.1038/s41598-017-08286-2 Full text in Research Archive. Show summary

  Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.

• Barth, Julia Maria Isis; Damerau, Malte; Matschiner, Michael; Jentoft, Sissel & Hanel, Reinhold (2017). Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations. Genome Biology and Evolution (GBE).  ISSN 1759-6653.  9(4), s 1084- 1098 . doi: 10.1093/gbe/evx067 Full text in Research Archive.
• 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, s 1- 13 . doi: 10.1038/sdata.2016.132 Full text in Research Archive.
• 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 Full text in Research Archive. Show summary

  Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the “fossilized birth-death” model and “total-evidence dating”. While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth-death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes.

• 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 Show summary

  How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation-related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time-calibrated species tree based on whole-genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre-to-periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination density and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chromosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between nonphysically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, differences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spectacular cichlid diversity observed today.

• 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 Full text in Research Archive.
• 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.  66(4), s 531- 550 . doi: 10.1093/sysbio/syw069 Show summary

  Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.

• 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 (2019). Accuracy and precision of phylogenomic divergence-time estimates.
• Matschiner, Michael & Salzburger, Walter (2019). Evolution: Genomic Signatures of Mimicry and Mimicry of Genomic Signatures. Current Biology.  ISSN 0960-9822.  29, s R363- R365 . doi: 10.1016/j.cub.2019.04.015
• Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The impact of repetitive DNA on speciation rates in teleost fish.
• Barth, Julia Maria Isis; Star, Bastiaan; Matschiner, Michael; André, Carl; Knutsen, Halvor; Bradbury, Ian; Dierking, Jan; Petereit, Christoph; Righton, David; Metcalfe, Julian; Jakobsen, Kjetill Sigurd; Olsen, Esben Moland & Jentoft, Sissel (2017). Chromosomal rearrangements as barriers to homogenization in highly mobile fish.
• Barth, Julia Maria Isis; Star, Bastiaan; Matschiner, Michael; André, Carl; Knutsen, Halvor; Bradbury, Ian; Dierking, Jan; Petereit, Christoph; Righton, David; Metcalfe, Julian; Jakobsen, Kjetill Sigurd; Olsen, Esben Moland & Jentoft, Sissel (2017). Chromosomal rearrangements as barriers to homogenization in highly mobile fish.
• Matschiner, Michael (2017). Phylogenetic dating of cichlid radiations.
• 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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