Michael Matschiner

• Sommer-Trembo, Carolin; Santos, M Emília; Clark, Bethan; Werner, Marco; Fages, Antoine & Matschiner, Michael [Vis alle 13 forfattere av denne artikkelen] (2024). The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes. Science. ISSN 0036-8075. 384(6694), s. 470–475. doi: 10.1126/science.adj9228.
• Tsuboi, Masahito; Kopperud, Bjørn Tore; Matschiner, Michael; Grabowski, Mark Walter; Syrowatka, Christine & Pelabon, Christophe [Vis alle 7 forfattere av denne artikkelen] (2024). Antler Allometry, the Irish Elk and Gould Revisited. Evolutionary Biology. ISSN 0071-3260. doi: 10.1007/s11692-023-09624-1.
• Johannessen, Lars Erik; Johnsen, Arild; Koppetsch, Thore; Lifjeld, Jan Terje; Matschiner, Michael & Søli, Geir Einar Ellefsen [Vis alle 7 forfattere av denne artikkelen] (2023). Arctic Specimens in the Zoological Collections at the Natural History Museum, University of Oslo, Norway (NHMO). Collections: A Journal for Museum and Archives Professionals. ISSN 1550-1906. doi: 10.1177/15501906231167574. Vis sammendrag

  In the NHMO zoological collections, specimens from the Arctic include about 9,000 mammals and 7,100 birds, whereas the Insect Collection holds about 105,000 specimens plus more than hundred jars with unsorted material. The Fish Collection contains approximately 1,400 specimens, while the Herptile Collection (amphibians & reptiles) holds only thirty-one specimens of three taxa. Many of these specimens originate from expeditions to E Greenland, N Canada, Svalbard, Novaya Zemlya, Finnmark, and NE Siberia in the period 1898 to 1966. Furthermore, the DNA Bank has about 5,600 tissue and extracted DNA samples, mostly sampled from wild animals during the last decades but also from specimens in the voucher collections. Most of the Arctic specimens have been digitized and are available in online data portals like GBIF, except for the Insect Collection, where only the type material and about 30 percent of the total specimens are digitized.

• Reinar, William Brynildsen; Tørresen, Ole K.; Nederbragt, Lex; Matschiner, Michael; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2023). Teleost genomic repeat landscapes in light of diversification rates and ecology. Mobile DNA. ISSN 1759-8753. 14(1), s. 1–12. doi: 10.1186/s13100-023-00302-9. Fulltekst i vitenarkiv
• Lifjeld, Jan Terje; Hernando, Miguel de Gabriel; Marcos, Benito Fuertes; Grønstøl, Gaute; Anmarkrud, Jarl Andreas & Matschiner, Michael [Vis alle 7 forfattere av denne artikkelen] (2023). Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation? Evolution. ISSN 0014-3820. 77(11), s. 2352–2364. doi: 10.1093/evolut/qpad146.
• Yu, Lei; Khachaturyan, Marina; Matschiner, Michael; Healey, Adam; Bauer, Diane & Cameron, Brenda [Vis alle 37 forfattere av denne artikkelen] (2023). Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina). Nature Plants. ISSN 2055-026X. 9(8), s. 1207–1220. doi: 10.1038/s41477-023-01464-3. Fulltekst i vitenarkiv
• Bista, Iliana; Wood, Jonathan M. D.; Desvignes, Thomas; McCarthy, Shane A.; Matschiner, Michael & Ning, Zemin [Vis alle 21 forfattere av denne artikkelen] (2023). Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nature Communications. ISSN 2041-1723. 14(1). doi: 10.1038/s41467-023-38567-6.
• Barth, Julia Maria Isis; Handley, Scott A.; Kintzl, Daniel; Leonard, Guy; Malinsky, Milan & Matschiner, Michael [Vis alle 10 forfattere av denne artikkelen] (2023). The history and organization of the Workshop on Population and Speciation Genomics. Evolution: Education and Outreach. ISSN 1936-6426. 16(1). doi: 10.1186/s12052-023-00182-w.
• Schiavon, Luca; Negrisolo, Enrico; Battistotti, Alessandra; Lucassen, Magnus; Damerau, Malte & Harms, Lars [Vis alle 11 forfattere av denne artikkelen] (2023). Species identification and population genetics of the Antarctic fish genera Lepidonotothen and Nototheniops (Perciformes, Notothenioidei). Zoologica Scripta. ISSN 0300-3256. 52(2), s. 136–153. doi: 10.1111/zsc.12580.
• Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar & Bleidorn, Christoph [Vis alle 55 forfattere av denne artikkelen] (2023). How genomics can help biodiversity conservation. Trends in Genetics. ISSN 0168-9525. 39(7), s. 545–559. doi: 10.1016/j.tig.2023.01.005. Fulltekst i vitenarkiv Vis sammendrag

  The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

• Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano & Bleidorn, Christoph [Vis alle 59 forfattere av denne artikkelen] (2022). The era of reference genomes in conservation genomics. Trends in Ecology & Evolution. ISSN 0169-5347. 37(3), s. 197–202. doi: 10.1016/j.tree.2021.11.008. Fulltekst i vitenarkiv
• Muschick, Moritz; Nikolaeva, Ekaterina; Rüber, Lukas & Matschiner, Michael (2022). The mitochondrial genome of the red icefish (Channichthys rugosus) casts doubt on its species status. Polar Biology. ISSN 0722-4060. 45(10), s. 1541–1552. doi: 10.1007/s00300-022-03083-8. Fulltekst i vitenarkiv
• Baumdicker, Franz; Bisschop, Gertjan; Goldstein, Daniel; Gower, Graham; Ragsdale, Aaron P. & Tsambos, Georgia [Vis alle 32 forfattere av denne artikkelen] (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics. ISSN 0016-6731. 220(3). doi: 10.1093/genetics/iyab229. Fulltekst i vitenarkiv
• Matschiner, Michael; Barth, Julia Maria Isis; Tørresen, Ole K.; Star, Bastiaan; Baalsrud, Helle Tessand & Brieuc, Marine Servane Ono [Vis alle 10 forfattere av denne artikkelen] (2022). Supergene origin and maintenance in Atlantic cod. Nature Ecology and Evolution. ISSN 2397-334X. 6(4), s. 469–481. doi: 10.1038/s41559-022-01661-x. Fulltekst i vitenarkiv
• Pinsky, Malin L.; Eikeset, Anne Maria; Helmerson, Cecilia Jenny Margareta Thomas; Bradbury, Ian R.; Bentzen, Paul & Morris, Corey [Vis alle 17 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• Vilaça, Sibelle; Piccinno, Riccardo; Rota-Stabelli, Omar; Gabrielli, Maëva; Benazzo, Andrea & Matschiner, Michael [Vis alle 10 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv Vis sammendrag

  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. 7, s. 1–16. doi: 10.1126/sciadv.abe8215. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 12 forfattere av denne artikkelen] (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. Vis sammendrag

  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.

• 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. Fulltekst i vitenarkiv Vis sammendrag

  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.

• 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. Vis sammendrag

  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.

• Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael & Baalsrud, Helle Tessand [Vis alle 12 forfattere av denne artikkelen] (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. Vis sammendrag

  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.

• Barth, Julia Maria Isis; Gubili, Chrysoula; Matschiner, Michael; Tørresen, Ole K.; Watanabe, Shun & Egger, Bernd [Vis alle 11 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv Vis sammendrag

  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.

• Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F. & Guo, Baocheng [Vis alle 9 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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. Fulltekst i vitenarkiv Vis sammendrag

  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). 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. Fulltekst i vitenarkiv
• Bouckaert, Remco; Vaughan, Timothy G; Barrido-Sottani, Joëlle; Duchêne, Sebastián; Fourment, Mathieu & Gavryushkina, Alexandra [Vis alle 25 forfattere av denne artikkelen] (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), s. 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. [Vis alle 18 forfattere av denne artikkelen] (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.
• Ceballos, Santiago; Roesti, Marius; Matschiner, Michael; Fernandez, Daniel A; Damerau, Malte & Hanel, Reinhold [Vis alle 7 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K.; Hadiaty, Renny Kurnia & Yaakob, Norsham [Vis alle 10 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• Langangen, Øystein; Färber, Leonie Anette; Stige, Leif Christian; Diekert, Florian Klaus; Barth, Julia Maria Isis & Matschiner, Michael [Vis alle 11 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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.
• Runemark, Anna; Trier, Cassandra Nicole; Eroukhmanoff, Fabrice; Hermansen, Jo Skeie; Matschiner, Michael & Ravinet, Mark [Vis alle 8 forfattere av denne artikkelen] (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.
• 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 [Vis alle 10 forfattere av denne artikkelen] (2017). Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Scientific Reports. ISSN 2045-2322. 7, s. 1–10. doi: 10.1038/s41598-017-08286-2. Fulltekst i vitenarkiv Vis sammendrag

  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. Fulltekst i vitenarkiv
• 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. Fulltekst i vitenarkiv
• Matschiner, Michael; Musilová, Zuzana; Barth, Julia Maria Isis; Starostová, Zuzana; Salzburger, Walter & Steel, Mike [Vis alle 7 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 13 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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. Vis sammendrag

  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), s. 531–550. doi: 10.1093/sysbio/syw069. Vis sammendrag

  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), s. 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, 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. I Riesch, Rüdiger; Tobler, Michael & Plath, Martin (Red.), Extremophile Fishes. Springer. ISSN 978-3-319-13362-1. s. 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, s. 56–71. doi: 10.1016/j.ympev.2014.10.009.

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• Yu, Lei; Khachaturyan, Marina; Matschiner, Michael; Healey, Adam; Bauer, Diane & Cameron, Brenda [Vis alle 37 forfattere av denne artikkelen] (2023). Author Correction: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina) (Nature Plants, (2023), 9, 8, (1207-1220), 10.1038/s41477-023-01464-3). Nature Plants. ISSN 2055-026X. 9(8). doi: 10.1038/s41477-023-01504-y.
• Matschiner, Michael (2021). Museum specimens tell the history of rhinoceroses. Cell. ISSN 0092-8674. doi: 10.1016/j.cell.2021.08.026. Vis sammendrag

  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, 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.
• Matschiner, Michael (2017). Phylogenetic dating of cichlid radiations.
• Barth, Julia Maria Isis; Star, Bastiaan; Matschiner, Michael; André, Carl; Knutsen, Halvor & Bradbury, Ian [Vis alle 13 forfattere av denne artikkelen] (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 [Vis alle 13 forfattere av denne artikkelen] (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 [Vis alle 12 forfattere av denne artikkelen] (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 [Vis alle 11 forfattere av denne artikkelen] (2014). Population differentiation and local adaptation in Atlantic cod.

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