Michael Matschiner

• Muschick, Moritz; Rüber, Lukas & Matschiner, Michael (2025). Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae). Molecular Phylogenetics and Evolution. ISSN 1055-7903. 211. doi: 10.1016/j.ympev.2025.108406. Full text in Research Archive Show summary

  Lophichthys boschmai, the only member of the family Lophichthyidae, is an elusive lophiiform fish whose phylogenetic associations are debated. This family is among the last two vertebrate families lacking DNA sequence data, primarily due to the species’ rarity, lack of fresh material and challenges associated with sequencing formalin-treated museum specimens. In this study, we provide mitochondrial and nuclear DNA sequences obtained from two museum specimens of Lophichthys boschmai. Employing ancient DNA techniques, we successfully extracted and analyzed the degraded and fragmented DNA. Our findings, derived from both mitochondrial genomes and nuclear ultra-conserved elements (UCE), reveal the Lophichthyidae as sister lineage to Tathicarpidae within the Antennarioidei. This study showcases the use of whole-genome “shotgun” sequencing data from formalin-fixed museum specimens in the context of an available UCE dataset. Given the enhanced versatility in data reusability this approach offers, we suggest it should be a favored approach when studying rare specimens.

• Delrieu-Trottin, Erwan; Koppetsch, Thore; Rønning, Ann-Helen & Matschiner, Michael (2025). Thor Heyerdahl's Legacy: Ichthyological and Herpetological Collection on Fatu Hiva (Marquesas Islands) in 1937. Pacific Science. ISSN 0030-8870. 78(4), p. 373–385. doi: 10.2984/78.4.2. Full text in Research Archive Show summary

  The Norwegian explorer and writer Thor Heyerdahl is most famous for his 1947 Kon-Tiki expedition, a journey performed on a balsa raft, drifting from South America to French Polynesia. However, his exploration of the Pacific to answer questions revolving around the colonization of isolated islands began earlier, in December 1936, when he and his wife, Liv, traveled to Fatu Hiva, one of the most remote locations of the Marquesas Islands. During their year-long stay, Thor Heyerdahl and Liv Torp-Heyerdahl collected ichthyological and herpetological material that has since remained without analysis for more than 80 yr at the Natural History Museum in Oslo. Here, we provide the first identifications of the collected material. Ninety-four specimens have been identified to the species level, three to the genus level, and six specimens remain at the family level or above. The collection comprises mostly fishes, with 66 reef fish specimens encompassing at least 14 species and 27 freshwater specimens covering at least 6 species. Ten specimens of reptiles were also collected by Thor Heyerdahl, including four species of both geckos (Gehyra insulensis and G. oceanica) and skinks (Emoia cyanura and Ornithuroscincus noctua). Many specimens are juveniles, making accurate identification challenging. Incorporating molecular data for species identification is a promising direction for future studies. The expedition marked a turning point in Heyerdahl's career, shifting his focus from zoology to anthropology and setting the stage for his later research on human migration and Pacific cultural connections.

• Schmid, Sarah; Straube, Nicolas; Albouy, Camille; Delling, Bo; Maclaine, James & Matschiner, Michael [Show all 14 contributors for this article] (2025). Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring. BioScience. ISSN 0006-3568. 75(12), p. 1083–1095. doi: 10.1093/biosci/biaf140. Full text in Research Archive Show summary

  Biodiversity changes due to human activities highlight the need for efficient biodiversity monitoring approaches. Environmental DNA (eDNA) metabarcoding offers a noninvasive method used for biodiversity monitoring and ecosystem assessment, but its accuracy depends on comprehensive DNA reference databases. Natural history collections often contain rare or difficult-to-obtain samples that can serve as a valuable resource to fill gaps in eDNA reference databases. In the present article, we discuss the utility of specimens from natural history collections in supporting future eDNA applications. Museomics—the application of -omics techniques to museum specimens—offers a promising avenue for improving eDNA reference databases by increasing species coverage. Furthermore, museomics can provide transferable methodological advancements for extracting genetic material from samples with low and degraded DNA. The integration of natural history collections, museomics, and eDNA approaches has the potential to significantly improve our understanding of global biodiversity, highlighting the continued importance of natural history collections.

• Garmann-Aarhus, Benedicte; Nikolaeva, Ekaterina; Desvignes, Thomas; Straube, Nicolas & Matschiner, Michael (2025). Museomic analyses clarify species diversity in the icefish genus Channichthys. Polar Biology. ISSN 0722-4060. 48(1). doi: 10.1007/s00300-025-03349-x. Full text in Research Archive Show summary

  The rapid diversification of notothenioid fishes in Antarctic waters is a prime example of the process of adaptive radiation. Within around 10 million years, Antarctic notothenioids have diversified into over 100 species with a broad range of lifestyles and ecological adaptations. However, the exact number of species within this radiation has long been unclear. Particularly challenging is the taxonomy of the genus Channichthys, for which between one and nine species have been recognized by different authors. The putative species of this genus are known from a limited number of specimens, of which most were sampled decades ago. Here, we investigated the mitochondrial genomes of museum specimens representing the four species Unicorn Icefish (C. rhinoceratus), Red Icefish (C. rugosus), Sailfish Pike (C. velifer), and Charcoal Icefish (C. panticapaei), complemented by morphological analyses. All analyzed specimens were collected in the 1960s and 1970s and fixed in formaldehyde, and their DNA has been heavily degraded. Applying ancient-DNA protocols for DNA extraction and single-stranded library preparation, we were able to obtain sufficient endogenous DNA to reconstruct the mitochondrial genomes of one specimen per species. These mitochondrial genome sequences were nearly identical for the three specimens assigned to Unicorn Icefish, Red Icefish, and Sailfish Pike, while greater divergence was observed for the Charcoal Icefish specimens. We discuss possible explanations of the contrast between these molecular results and the recognizable morphological variation found among the four species, and recommend that at least the Charcoal Icefish be included in the list of valid notothenioid species.

• Koppetsch, Thore; Malinsky, Milan & Matschiner, Michael (2024). Towards Reliable Detection of Introgression in the Presence of Among‑Species Rate Variation. Systematic Biology. ISSN 1063-5157. 73(5), p. 769–788. doi: 10.1093/sysbio/syae028. Full text in Research Archive Show summary

  The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression—the exchange of genetic material through hybridization and backcrossing—are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report “ancient introgression”— referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.

• Hofmann, Sylvia; Rödder, Dennis; Tobias, Andermann; Matschiner, Michael; Riedel, Jendrian & Baniya, Chitra B [Show all 19 contributors for this article] (2024). Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae). Molecular Ecology. ISSN 0962-1083. 33(15). doi: 10.1111/mec.17446. Full text in Research Archive
• Sommer-Trembo, Carolin; Santos, M Emília; Clark, Bethan; Werner, Marco; Fages, Antoine & Matschiner, Michael [Show all 13 contributors for this article] (2024). The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes. Science. ISSN 0036-8075. 384(6694), p. 470–475. doi: 10.1126/science.adj9228. Full text in Research Archive
• Gracia, Alberto Valero; Roberts, Nickellaus G; Yap-Chiongco, Meghan; Capucho, Ana Teresa; Kocot, Kevin M & Matschiner, Michael [Show all 7 contributors for this article] (2024). First Chromosome-Level Genome Assembly of a Ribbon Worm from the Hoplonemertea Clade, Emplectonema gracile, and Its Structural Annotation. Genome Biology and Evolution (GBE). 16(7). doi: 10.1093/gbe/evae127. Full text in Research Archive Show summary

  Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome for a Hoplonemertea species is crucial. Such data will be highly useful for future investigations toward a better understanding of molecular ecology, venom evolution, and regeneration not only in Nemertea but also in other marine invertebrate phyla. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well suited for laboratory experimentation. The genome has an assembly size of 157.9 Mb. Hi-C scaffolding yielded chromosome-level scaffolds, with a scaffold N50 of 10.0 Mb and a score of 95.1% for complete BUSCO genes found as a single copy. Annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50.

• Burriel-Carranza, Bernat; Mochales-Riaño, Gabriel; Talavera, Adrián; Els, Johannes; Estarellas, Maria & Saadi, Saleh Al [Show all 10 contributors for this article] (2024). Clinging on the brink: Whole genomes reveal human-induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus). Molecular Ecology. ISSN 0962-1083. 33(15). doi: 10.1111/mec.17451. Full text in Research Archive
• Tsuboi, Masahito; Kopperud, Bjørn Tore; Matschiner, Michael; Grabowski, Mark Walter; Syrowatka, Christine & Pelabon, Christophe [Show all 7 contributors for this article] (2024). Antler Allometry, the Irish Elk and Gould Revisited. Evolutionary Biology. ISSN 0071-3260. 51, p. 149–165. doi: 10.1007/s11692-023-09624-1. Full text in Research Archive Show summary

  The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data on antler size in the Irish elk and combined these with comparative data from other deer to test the hypothesis that the gigantic antlers were the outcome of a positive allometry that constrained large-bodied deer to have proportionally even larger antlers. He concluded that the Irish elk had antlers as predicted for its size and interpreted this within his emerging framework of developmental constraints as an explanatory factor in evolution. Here we reanalyze antler allometry based on new morphometric data for 57 taxa of the family Cervidae. We also present a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast to Gould, we find that the antlers of Irish elk were larger than predicted from the allometry within the true deer, Cervini, as analyzed by Gould, but follow the allometry across Cervidae as a whole. After dissecting the discrepancy, we reject the allometric-constraint hypothesis because, contrary to Gould, we find no similarity between static and evolutionary allometries, and because we document extensive non-allometric evolution of antler size across the Cervidae.

• Hofmann, Sylvia; Podsiadlowski, Lars; Andermann, Tobias; Matschiner, Michael; Baniya, Chitra Bahadur & Litvinchuk, Spartak N [Show all 12 contributors for this article] (2024). The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota? Molecular Phylogenetics and Evolution. ISSN 1055-7903. 201. doi: 10.1016/j.ympev.2024.108166. Full text in Research Archive
• Vences, Miguel; Patmanidis, Stefanos; Schmidt, Jan-Christopher; Matschiner, Michael; Miralles, Aurélien & Renner, Susanne S. (2024). Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation. Bioinformatics Advances. 4(1). doi: 10.1093/bioadv/vbae083. Full text in Research Archive Show summary

  Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other datasets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).

• Omelchenko, Dmytro; Bitja-Nyom, Arnold Roger; Matschiner, Michael; Malinsky, Milan; Indermaur, Adrian & Salzburger, Walter [Show all 8 contributors for this article] (2024). Haemoglobin Gene Repertoire in Teleost and Cichlid Fishes Shaped by Gene Duplications and Genome Rearrangements. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.17559. Full text in Research Archive Show summary

  Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high-quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain a range of haemoglobin genes, from as few as five in fugu to as many as 43 in salmon, with the latter being the largest repertoire found in vertebrates. We find evidence that the teleost ancestor had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organisation of haemoglobin clusters in different teleost species. We further show that the evolution of paralogous rhbdf1 genes flanking both teleost clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environment plays role in species diversification. Our analysis of six cichlid genomes, including Pungu maclareni from the Barombi Mbo crater lake, for which we sequenced a representative genome, reveals 18–32 copies of the Hb genes, and elevated rates of non-synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how haemoglobin genes contribute to the adaptive potential of teleosts.

• Schiavon, Luca; Ceballos, Santiago G; Matschiner, Michael; Trucchi, Emiliano; Mesa, Mario La & Riginella, Emilio [Show all 14 contributors for this article] (2024). Limited interspecific gene flow in the evolutionary history of the icefish genus Chionodraco. ICES Journal of Marine Science. ISSN 1054-3139. 81(4), p. 676–686. doi: 10.1093/icesjms/fsae019. Full text in Research Archive Show summary

  Hybridization and introgression are recognized as mechanisms promoting genetic variability during evolutionary radiations. We examined the impact of introgression in the process of speciation, focusing on the Antarctic icefish genus Chionodraco. Our analyses confirmed that the three Chionodraco species (Chionodraco hamatus, Chionodraco myersi, and Chionodraco rastrospinosus) were genetically distinctive, despite signals of past interspecific gene flow between C. hamatus and C. myersi that likely occurred during interglacial periods. However, in this study, no recent hybrids were identified. The lack of contemporary hybridization may be due to life-history traits and the type of marker used in the analysis. Our study emphasizes the importance of genomic approaches to detect subtle patterns of past hybridization accurately and highlights the significance of historical climate events in the demographic and evolutionary history of Antarctic notothenioids. Polar regions, and especially the Antarctic Peninsula, are now experiencing the fastest climate changes due to global warming. Understanding the impact of past climate events is fundamental to trace current modifications in species’ genetic variability and distributions and predict future evolutionary trajectories. This knowledge is also vital for conservation efforts, including the implementation of marine protected areas.

• Lifjeld, Jan Terje; Hernando, Miguel de Gabriel; Marcos, Benito Fuertes; Grønstøl, Gaute; Anmarkrud, Jarl Andreas & Matschiner, Michael [Show all 7 contributors for this article] (2023). Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation? Evolution. ISSN 0014-3820. 77(11), p. 2352–2364. doi: 10.1093/evolut/qpad146. Full text in Research Archive
• Johannessen, Lars Erik; Johnsen, Arild; Koppetsch, Thore; Lifjeld, Jan Terje; Matschiner, Michael & Søli, Geir Einar Ellefsen [Show all 7 contributors for this article] (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. Full text in Research Archive Show summary

  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.

• Yu, Lei; Khachaturyan, Marina; Matschiner, Michael; Healey, Adam; Bauer, Diane & Cameron, Brenda [Show all 37 contributors for this article] (2023). Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina). Nature Plants. ISSN 2055-026X. 9(8), p. 1207–1220. doi: 10.1038/s41477-023-01464-3. Full text in Research Archive Show summary

  Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

• Barth, Julia Maria Isis; Handley, Scott A.; Kintzl, Daniel; Leonard, Guy; Malinsky, Milan & Matschiner, Michael [Show all 10 contributors for this article] (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. Full text in Research Archive Show summary

  With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of workshops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Český Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, explain the routine for workshop organization that we have optimized over the years, and describe the most important lessons that we have learned from it. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.

• Schiavon, Luca; Negrisolo, Enrico; Battistotti, Alessandra; Lucassen, Magnus; Damerau, Malte & Harms, Lars [Show all 11 contributors for this article] (2023). Species identification and population genetics of the Antarctic fish genera Lepidonotothen and Nototheniops (Perciformes, Notothenioidei). Zoologica Scripta. ISSN 0300-3256. 52(2), p. 136–153. doi: 10.1111/zsc.12580. Full text in Research Archive
• Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar & Bleidorn, Christoph [Show all 55 contributors for this article] (2023). How genomics can help biodiversity conservation. Trends in Genetics. ISSN 0168-9525. 39(7), p. 545–559. doi: 10.1016/j.tig.2023.01.005. Full text in Research Archive Show summary

  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.

• Bista, Iliana; Wood, Jonathan M. D.; Desvignes, Thomas; McCarthy, Shane A.; Matschiner, Michael & Ning, Zemin [Show all 21 contributors for this article] (2023). Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nature Communications. 14(1). doi: 10.1038/s41467-023-38567-6. Full text in Research Archive
• 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. 14(1), p. 1–12. doi: 10.1186/s13100-023-00302-9. Full text in Research Archive Show summary

  Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

• Matschiner, Michael; Barth, Julia Maria Isis; Tørresen, Ole K.; Star, Bastiaan; Baalsrud, Helle Tessand & Brieuc, Marine Servane Ono [Show all 10 contributors for this article] (2022). Supergene origin and maintenance in Atlantic cod. Nature Ecology and Evolution. 6(4), p. 469–481. doi: 10.1038/s41559-022-01661-x. Full text in Research Archive Show summary

  Abstract Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.

• 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), p. 1541–1552. doi: 10.1007/s00300-022-03083-8. Full text in Research Archive Show summary

  Abstract Antarctic notothenioid fishes are recognised as one of the rare examples of adaptive radiation in the marine system. Withstanding the freezing temperatures of Antarctic waters, these fishes have diversified into over 100 species within no more than 10–20 million years. However, the exact species richness of the radiation remains contested. In the genus Channichthys , between one and nine species are recognised by different authors. To resolve the number of Channichthys species, genetic information would be highly valuable; however, so far, only sequences of a single species, C. rhinoceratus , are available. Here, we present the nearly complete sequence of the mitochondrial genome of C. rugosus , obtained from a formalin-fixed museum specimen sampled in 1974. This sequence differs from the mitochondrial genome of C. rhinoceratus in no more than 27 positions, suggesting that the two species may be synonymous.

• Baumdicker, Franz; Bisschop, Gertjan; Goldstein, Daniel; Gower, Graham; Ragsdale, Aaron P. & Tsambos, Georgia [Show all 32 contributors for this article] (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics. ISSN 0016-6731. 220(3). doi: 10.1093/genetics/iyab229. Full text in Research Archive Show summary

  Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

• Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano & Bleidorn, Christoph [Show all 59 contributors for this article] (2022). The era of reference genomes in conservation genomics. Trends in Ecology & Evolution. ISSN 0169-5347. 37(3), p. 197–202. doi: 10.1016/j.tree.2021.11.008. Full text in Research Archive Show summary

  Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.

• Matschiner, Michael (2021). Museum specimens tell the history of rhinoceroses. Cell. ISSN 0092-8674. doi: 10.1016/j.cell.2021.08.026. Full text in Research Archive 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.

• 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. Full text in Research Archive 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.

• Taher, Athimed El; Ronco, Fabrizia; Matschiner, Michael; Salzburger, Walter & Böhne, Astrid (2021). Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes. Science Advances. 7, p. 1–16. doi: 10.1126/sciadv.abe8215. Full text in Research Archive 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.

• 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 (PNAS). ISSN 0027-8424. 118(15). doi: 10.1073/pnas.2025453118. Full text in Research Archive Show summary

  The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

• Ronco, Fabrizia; Matschiner, Michael; Böhne, Astrid; Boila, Anna; Büscher, Heinz H & Taher, Athimed El [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. Full text in Research Archive 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.

• 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. Full text in Research Archive 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. 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.

• 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. 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.

• 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 (PNAS). ISSN 0027-8424. 117(17), p. 9431–9439. doi: 10.1073/pnas.1916251117. Full text in Research Archive 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.

• 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. Full text in Research Archive
• 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. 19(1), p. 1–14. doi: 10.1186/s12862-019-1345-z. Full text in Research Archive Show summary

  Background The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species. Results We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance. Conclusions Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.

• 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 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.

• 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). 11(11), p. 3291–3308. doi: 10.1093/gbe/evz240. Full text in Research Archive Show summary

  The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.

• 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. 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. 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. 10. doi: 10.3389/fgene.2019.01064. Full text in Research Archive Show summary

  The fossilized birth–death (FBD) model allows the estimation of species divergence times from molecular and fossil information in a coherent framework of diversification and fossil sampling. Some assumptions of the FBD model, however, are difficult to meet in phylogenetic analyses of highly diverse groups. Here, I use simulations to assess the impact of extreme model violations, including diversified sampling of species and the exclusive use of the oldest fossils per clade, on divergence times estimated with the FBD model. My results demonstrate that selective sampling of fossils can produce dramatically overestimated divergence times when the FBD model is used for inference, due to an interplay of underestimates for the model parameters net diversification rate, turnover, and fossil-sampling proportion. In contrast, divergence times estimated with CladeAge, a method that uses information about the oldest fossils per clade together with estimates of sampling and diversification rates, are accurate under these conditions. Practitioners of Bayesian divergence-time estimation should therefore ensure that the dataset conforms to the expectations of the FBD model, or estimates of sampling and diversification rates should be obtained a priori so that CladeAge can be used for the inference.

• 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). 10(4), p. 1088–1103. doi: 10.1093/gbe/evy058. Full text in Research Archive Show summary

  The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

• 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 Show summary

  Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put forward to explain these changes: climate and harvesting. Climate could affect the distribution through, for example, spatial habitat shifts. Harvesting could affect the distribution through impacting the demographic structure. If demographic structure is important, theory predicts increasing spawner size with migration distance. Here, we evaluate these hypotheses with modern data from a period (2000–2016) of increasing temperature and recovering stock structure. We first analyze economic data from the Norwegian fisheries to investigate geographical differences in size of spawning fish among spawning grounds, as well as interannual differences in mean latitude of spawning in relation to changes in temperature and demographic parameters. Second, we analyze genetically determined fish sampled at the spawning grounds to unambiguously separate between migratory NEA cod and potentially smaller sized coastal cod of local origin. Our results indicate smaller spawners farther away from the feeding grounds, hence not supporting the hypothesis that harvesting is a main driver for the contemporary spawning ground distribution. We find a positive correlation between annual mean spawning latitude and temperature. In conclusion, based on contemporary data, there is more support for climate compared to harvesting in shaping spawning ground distribution in this major fish stock in the North Atlantic Ocean.

• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. 2(3), p. 549–556. doi: 10.1038/s41559-017-0437-7. 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. 4, p. 1–13. doi: 10.1038/sdata.2016.132. Full text in Research Archive Show summary

  Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts.

• 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). 9(4), p. 1084–1098. doi: 10.1093/gbe/evx067. Full text in Research Archive Show summary

  Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.

• 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. 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.

• 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 Show summary

  Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.

• 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. Full text in Research Archive
• 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. Full text in Research Archive 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.

• 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. Full text in Research Archive 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.

• 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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 9783319133621. p. 35–57. doi: 10.1007/978-3-319-13362-1_3. Full text in Research Archive

View all works in NVA

• Garmann-Aarhus, Benedicte; Nikolaeva, Ekaterina; Desvignes, Thomas; Straube, Nicolas & Matschiner, Michael (2024). Museomics informs about species diversity within the adaptive radiation of Antarctic notothenioid fishes. Full text in Research Archive
• Yu, Lei; Khachaturyan, Marina; Matschiner, Michael; Healey, Adam; Bauer, Diane & Cameron, Brenda [Show all 37 contributors for this article] (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), p. 1370–1370. doi: 10.1038/s41477-023-01504-y. Full text in Research Archive
• Matschiner, Michael (2019). Accuracy and precision of phylogenomic divergence-time estimates. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• Matschiner, Michael; Star, Bastiaan; Barth, Julia Maria Isis; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2017). Genomic rearrangements a phylogenetic approach. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• Matschiner, Michael (2017). Phylogenetic dating of cichlid radiations. Full text in Research Archive
• 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. Full text in Research Archive
• Matschiner, Michael (2015). Inversions or Introgression: The origin of high-divergence genomic regions in Atlantic cod. Full text in Research Archive
• 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? Full text in Research Archive
• 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. Full text in Research Archive

View all works in NVA