Michael Matschiner

• Pinsky, Malin L.; Eikeset, Anne Maria; Helmerson, Cecilia Jenny Margareta Thomas; Bradbury, Ian R.; Bentzen, Paul & Morris, Corey [Show all 17 contributors for this article] (2021). Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 118(15). doi: 10.1073/pnas.2025453118. Full text in Research Archive
• Vilaça, Sibelle; Piccinno, Riccardo; Rota-Stabelli, Omar; Gabrielli, Maëva; Benazzo, Andrea & Matschiner, Michael [Show all 10 contributors for this article] (2021). Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.16113. Show summary

  Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%–42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.

• El Taher, Athimed; Ronco, Fabrizia; Matschiner, Michael; Salzburger, Walter & Böhne, Astrid (2021). Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes. Science Advances. ISSN 2375-2548. doi: 10.1126/sciadv.abe8215. Show summary

  Sex is a fundamental trait determined by environmental and/or genetic factors, including sex chromosomes. Sex chromosomes are studied in species scattered across the tree of life, yet little is known about tempo and mode of sex chromosome evolution among closely related species. Here, we examine sex chromosome evolution in the adaptive radiation of cichlid fishes in Lake Tanganyika. Through the analysis of male and female genomes from 244 cichlid taxa (189 described species with 5 represented with two local variants/populations; 50 undescribed species) and of 396 multitissue transcriptomes from 66 taxa, we identify signatures of sex chromosomes in 79 taxa, involving 12 linkage groups. We find that Tanganyikan cichlids have the highest rates of sex chromosome turnover and heterogamety transitions known to date. We show that sex chromosome recruitment is not at random. Moreover convergently emerged sex chromosomes in cichlids support the “limited options” hypothesis of sex chromosome evolution.

• Ronco, Fabrizia; Matschiner, Michael; Böhne, Astrid; Boila, Anna; Büscher, Heinz H & El Taher, Athimed [Show all 12 contributors for this article] (2020). Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature. ISSN 0028-0836. 589, p. 76–81. doi: 10.1038/s41586-020-2930-4.
• 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
• 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), p. 584–595. doi: 10.1111/1755-0998.13265.
• Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael & Baalsrud, Helle Tessand [Show all 12 contributors for this article] (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), p. 9431–9439. doi: 10.1073/pnas.1916251117.
• Barth, Julia Maria Isis; Gubili, Chrysoula; Matschiner, Michael; Tørresen, Ole K.; Watanabe, Shun & Egger, Bernd [Show all 11 contributors for this article] (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
• Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F. & Guo, Baocheng [Show all 9 contributors for this article] (2019). A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome . Genome Biology and Evolution (GBE). ISSN 1759-6653. 11(11), p. 3291–3308. doi: 10.1093/gbe/evz240. 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, p. 1–5. doi: 10.1016/j.ympev.2019.106646. Full text in Research Archive
• 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
• Bouckaert, Remco; Vaughan, Timothy G; Barrido-Sottani, Joëlle; Duchêne, Sebastián; Fourment, Mathieu & Gavryushkina, Alexandra [Show all 25 contributors for this article] (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.
• Matschiner, Michael (2019). Gondwanan vicariance or trans-Atlantic dispersal of cichlid fishes: a review of the molecular evidence. Hydrobiologia. ISSN 0018-8158. 832(1), p. 9–37. doi: 10.1007/s10750-018-3686-9.
• Musilova, Zuzana; Cortesi, Fabio; Matschiner, Michael; Davies, Wayne I. L.; Patel, Jagdish Suresh & Stieb, Sara M. [Show all 18 contributors for this article] (2019). Vision using multiple distinct rod opsins in deep-sea fishes. Science. ISSN 0036-8075. 364(6440), p. 588–592. doi: 10.1126/science.aav4632.
• Ceballos, Santiago; Roesti, Marius; Matschiner, Michael; Fernandez, Daniel A; Damerau, Malte & Hanel, Reinhold [Show all 7 contributors for this article] (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), p. 1–14. doi: 10.1186/s12862-019-1345-z. Full text in Research Archive
• Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K.; Hadiaty, Renny Kurnia & Yaakob, Norsham [Show all 10 contributors for this article] (2018). The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biology and Evolution (GBE). ISSN 1759-6653. 10(4), p. 1088–1103. doi: 10.1093/gbe/evy058. Full text in Research Archive
• Langangen, Øystein; Färber, Leonie Anette; Stige, Leif Christian; Diekert, Florian Klaus; Barth, Julia Maria Isis & Matschiner, Michael [Show all 11 contributors for this article] (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), p. 134–143. doi: 10.1111/gcb.14474. 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), p. 681–699. doi: 10.1093/sysbio/syy006.
• Runemark, Anna; Trier, Cassandra Nicole; Eroukhmanoff, Fabrice; Hermansen, Jo Skeie; Matschiner, Michael & Ravinet, Mark [Show all 8 contributors for this article] (2018). Variation and constraints in hybrid genome formation. Nature Ecology and Evolution. ISSN 2397-334X. 2(3), p. 549–556. doi: 10.1038/s41559-017-0437-7.
• 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), p. 145–157. doi: 10.1093/sysbio/syx059.
• Baalsrud, Helle Tessand; Voje, Kjetil L.; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Matschiner, Michael & Malmstrøm, Martin [Show all 10 contributors for this article] (2017). Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Scientific Reports. ISSN 2045-2322. 7, p. 1–10. 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), p. 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, p. 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 [Show all 7 contributors for this article] (2017). Bayesian phylogenetic estimation of clade ages supports trans-Atlantic dispersal of cichlid fishes. Systematic Biology. ISSN 1063-5157. 66(1), p. 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.

• Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav & Hansen, Thomas F [Show all 13 contributors for this article] (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics. ISSN 1061-4036. 48(10), p. 1204–1210. doi: 10.1038/ng.3645. Full text in Research Archive
• 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), p. 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.

• 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), p. 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.

• Matschiner, Michael (2016). Fitchi: Haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics. ISSN 1367-4803. 32(8), p. 1250–1252. doi: 10.1093/bioinformatics/btv717.
• 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, p. 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 Riesch, Rüdiger; Tobler, Michael & Plath, Martin (Ed.), Extremophile Fishes. Springer. ISSN 978-3-319-13362-1. p. 35–57. doi: 10.1007/978-3-319-13362-1_3.
• 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, p. 56–71. doi: 10.1016/j.ympev.2014.10.009.

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• Matschiner, Michael (2021). Museum specimens tell the history of rhinoceroses. Cell. ISSN 0092-8674. doi: 10.1016/j.cell.2021.08.026. Show summary

  Rhinoceroses are facing an uncertain future due to human-induced population-size reductions. In this issue of Cell, Liu et al. analyze rhinoceros genomes to study their past and find support for an early divergence between African and Asian species, signatures of past hybridization, and evidence of loss of genetic diversity.

• 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, p. 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.
• Matschiner, Michael (2017). Phylogenetic dating of cichlid radiations.
• Barth, Julia Maria Isis; Star, Bastiaan; Matschiner, Michael; André, Carl; Knutsen, Halvor & Bradbury, Ian [Show all 13 contributors for this article] (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 [Show all 13 contributors for this article] (2017). Chromosomal rearrangements as barriers to homogenization in highly mobile fish.
• 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 [Show all 12 contributors for this article] (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 [Show all 11 contributors for this article] (2014). Population differentiation and local adaptation in Atlantic cod.

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