Mark Ravinet

• Ålund, Murielle; Cenzer, Meredith; Bierne, Nicolas; Boughman, Janette W.; Cerca Monteiro De Oliveira, José Pedro & Comerford, Mattheau S. [Vis alle 15 forfattere av denne artikkelen] (2023). Anthropogenic Change and the Process of Speciation. Cold Spring Harbor Perspectives in Biology. ISSN 1943-0264. 15(12), s. 1–24. doi: 10.1101/cshperspect.a041455.
• Choquet, Marvin ; Lizano, Apollo Marco Dalonos; Le Moan, Alan; Ravinet, Mark; Dhanasiri, Anusha & Hoarau, Galice Guillaume (2023). Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus. Molecular Ecology. ISSN 0962-1083. s. 6854–6873. doi: 10.1111/mec.17183. Fulltekst i vitenarkiv
• Kinneberg, Vilde Bruhn; Lü, Dabao Sun; Peris, David; Ravinet, Mark & Skrede, Inger (2023). Introgression between highly divergent fungal sister species. Journal of Evolutionary Biology. ISSN 1010-061X. 36(8), s. 1133–1149. doi: 10.1111/jeb.14190. Fulltekst i vitenarkiv
• Nilsson, Pernille; Ravinet, Mark; Cui, Yujun; Berg, Paul Ragnar; Zhang, Yujiang & Guo, Rong [Vis alle 17 forfattere av denne artikkelen] (2022). Polygenic plague resistance in the great gerbil uncovered by population sequencing. PNAS Nexus. ISSN 2752-6542. 1(5). doi: 10.1093/pnasnexus/pgac211.
• Sætre, Camilla Lo Cascio; Rönkä, Katja; Ravinet, Mark; Vitulano, Severino; Caldarella, Matteo & Procházka, Petr [Vis alle 13 forfattere av denne artikkelen] (2022). Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus). bioRxiv. ISSN 2692-8205. doi: 10.1101/2022.11.28.518135.
• Koch, Eva L.; Ravinet, Mark; Westram, Anja Marie; Johannesson, Kerstin & Butlin, Roger K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Evolution. ISSN 0014-3820. doi: 10.1111/evo.14602.
• Papoli Yazdi, Homa; Ravinet, Mark; Rowe, Melissah; Sætre, Glenn-Peter; Guldvog, Caroline Øien & Eroukhmanoff, Fabrice [Vis alle 9 forfattere av denne artikkelen] (2022). Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow. Molecular Ecology. ISSN 0962-1083. 31(15), s. 4067–4077. doi: 10.1111/mec.16572. Fulltekst i vitenarkiv
• Cuevas, Angelica; Eroukhmanoff, Fabrice; Ravinet, Mark; Sætre, Glenn-Peter & Runemark, Anna (2022). Predictors of genomic differentiation within a hybrid taxon. PLoS Genetics. ISSN 1553-7390. 18(2). doi: 10.1371/journal.pgen.1010027. Fulltekst i vitenarkiv
• Sowersby, Will; Cerca, José; Wong, Bob B. M.; Lehtonen, Topi K.; Chapple, David G. & Leal-Cardín, Mariana [Vis alle 8 forfattere av denne artikkelen] (2021). Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation. Molecular Ecology. ISSN 0962-1083. 30, s. 5551–5571. doi: 10.1111/mec.16139.
• Stankowski, Sean & Ravinet, Mark (2021). Defining the speciation continuum. Evolution. ISSN 0014-3820. 75(6), s. 1256–1273. doi: 10.1111/evo.14215. Fulltekst i vitenarkiv
• Cerca, José; Colon, Angel G. Rivera; Ferreira, Mafalda S.; Ravinet, Mark; Nowak, Michael & Catchen, Julian M. [Vis alle 7 forfattere av denne artikkelen] (2021). Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ. ISSN 2167-8359. 9. doi: 10.7717/peerj.10896. Fulltekst i vitenarkiv
• Sowersby, Will; Lehtonen, Topi K.; Ravinet, Mark; Barluenga, Marta & Wong, Bob B. M. (2020). Resource trait specialisation in an introduced fish population with reduced genetic diversity. Biological Invasions. ISSN 1387-3547. 22, s. 2447–2460. doi: 10.1007/s10530-020-02264-y. Fulltekst i vitenarkiv
• Cuevas, Angelica; Ravinet, Mark; Sætre, Glenn-Peter & Eroukhmanoff, Fabrice (2020). Intraspecific genomic variation and local adaptation in a young hybrid species. Molecular Ecology. ISSN 0962-1083. 00, s. 791–809. doi: 10.1111/mec.15760. Fulltekst i vitenarkiv
• Yoshida, Kohta; Ravinet, Mark; Makino, Takashi; Toyoda, Atsushi; Kokita, Tomoyuki & Mori, Seiichi [Vis alle 7 forfattere av denne artikkelen] (2020). Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations. Genome Biology and Evolution (GBE). ISSN 1759-6653. 12(4), s. 479–492. doi: 10.1093/gbe/evaa065. Fulltekst i vitenarkiv
• Ferrari, Giada; Neukamm, Judith; Baalsrud, Helle Tessand; Breidenstein, Abagail; Ravinet, Mark & Phillips, Carina [Vis alle 9 forfattere av denne artikkelen] (2020). Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philosophical Transactions of the Royal Society of London. Biological Sciences. ISSN 0962-8436. 375(1812), s. 1–9. doi: 10.1098/rstb.2019.0572. Fulltekst i vitenarkiv
• Rowe, Melissah; Whittington, Emma; Borziak, Kirill; Ravinet, Mark; Eroukhmanoff, Fabrice & Sætre, Glenn-Peter [Vis alle 7 forfattere av denne artikkelen] (2019). Molecular diversification of the seminal fluid proteome in a recently diverged passerine species pair. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 37(2), s. 488–506. doi: 10.1093/molbev/msz235. Fulltekst i vitenarkiv
• Faria, R; Chaube, P; Morales, Hernan E; Larsson, Tomas; Lemmon, AR & Lemmon, Emily Moriarty [Vis alle 12 forfattere av denne artikkelen] (2018). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. ISSN 0962-1083. 28(6), s. 1375–1393. doi: 10.1111/mec.14972. Fulltekst i vitenarkiv
• Westram, AM; Rafajlovic, M; Chaube, P; Faria, R; Larsson, Tomas & Panova, Marina [Vis alle 11 forfattere av denne artikkelen] (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. ISSN 2056-3744. 2(6), s. 297–309. doi: 10.1002/evl3.74. Fulltekst i vitenarkiv Vis sammendrag

  Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system‐specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome‐wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non‐neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non‐neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.

• Ravinet, Mark (2018). Notes from a snail island: Littorinid evolution and adaptation. Molecular Ecology. ISSN 0962-1083. 27(13), s. 2781–2789. doi: 10.1111/MEC.14730. Fulltekst i vitenarkiv Vis sammendrag

  The most successful study systems are built on a foundation of decades of research on the basic biology, ecology and life history of the organisms in question. Combined with new technologies, this can provide a formidable means to address important issues in evolutionary biology and molecular ecology. Littorinid marine snails are a good example of this, with a rich literature on their taxonomy, speciation, thermal tolerance and behavioural adaptations. In August 2017, an international meeting on Littorinid evolution was held at the Tjärnö Marine Research Laboratory in Western Sweden. In this meeting review, I provide a summary of some of the exciting work on parallel evolution, sexual selection and adaptation to environmental stress presented there. I argue that newly available genomic resources present an opportunity for integrating the traditionally divergent fields of speciation and environmental adaptation in Littorinid research.

• Ravinet, Mark; Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Aliabadian, Mansour; Gavrilov, Andrey & Sætre, Glenn-Peter (2018). Signatures of human-commensalism in the house sparrow genome. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 285(1884), s. 1–10. doi: 10.1098/rspb.2018.1246. Fulltekst i vitenarkiv
• 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.
• Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao & Kitano, Jun (2018). The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression. PLoS Genetics. ISSN 1553-7390. 14(5), s. 1–32. doi: 10.1371/journal.pgen.1007358. Fulltekst i vitenarkiv
• Østbye, Kjartan; Taugbøl, Annette; Ravinet, Mark; Harrod, Chris; Pettersen, Ruben Alexander & Bernatchez, Louis [Vis alle 7 forfattere av denne artikkelen] (2018). Ongoing niche differentiation under high gene flow in a polymorphic brackish water threespine stickleback (Gasterosteus aculeatus) population. BMC Evolutionary Biology. ISSN 1471-2148. 18(14), s. 1–18. doi: 10.1186/s12862-018-1128-y. Fulltekst i vitenarkiv Vis sammendrag

  Background: Marine threespine sticklebacks colonized and adapted to brackish and freshwater environments since the last Pleistocene glacial. Throughout the Holarctic, three lateral plate morphs are observed; the low, partial and completely plated morph. We test if the three plate morphs in the brackish water Lake Engervann, Norway, differ in body size, trophic morphology (gill raker number and length), niche (stable isotopes; δ15N, δ13C, and parasites (Theristina gasterostei, Trematoda spp.)), genetic structure (microsatellites) and the lateral-plate encoding Stn382 (Ectodysplasin) gene. We examine differences temporally (autumn 2006/spring 2007) and spatially (upper/lower sections of the lake – reflecting low versus high salinity). Results: All morphs belonged to one gene pool. The complete morph was larger than the low plated, with the partial morph intermediate. The number of lateral plates ranged 8–71, with means of 64.2 for complete, 40.3 for partial, and 14.9 for low plated morph. Stickleback δ15N was higher in the lower lake section, while δ13C was higher in the upper section. Stickleback isotopic values were greater in autumn. The low plated morph had larger variances in δ15N and δ13C than the other morphs. Sticklebacks in the upper section had more T. gasterostei than in the lower section which had more Trematoda spp. Sticklebacks had less T. gasterostei, but more Trematoda spp. in autumn than spring. Sticklebacks with few and short rakers had more T. gasterostei, while sticklebacks with longer rakers had more Trematoda. spp. Stickleback with higher δ15N values had more T. gasterostei, while sticklebacks with higher δ15N and δ13C values had more Trematoda spp. The low plated morph had fewer Trematoda spp. than other morphs. Conclusions: Trait-ecology associations may imply that the three lateral plate morphs in the brackish water lagoon of Lake Engervann are experiencing ongoing divergent selection for niche and migratory life history strategies under high gene flow. As such, the brackish water zone may generally act as a generator of genomic diversity to be selected upon in the different environments where threespine sticklebacks can live. Adaptation, Ectodysplasin, Evolution, Gill raker, Natural selection, Panmixia, Stable isotope analyses, Stn382, Theristina gasterostei, Trematoda spp

• Stuart, Yoel E.; Veen, Thor; Weber, Jesse N.; Hanson, Dieta; Ravinet, Mark & Lohman, Brian K. [Vis alle 15 forfattere av denne artikkelen] (2017). Contrasting effects of environment and genetics generate a continuum of parallel evolution. Nature Ecology and Evolution. ISSN 2397-334X. 1:0158(6), s. 1–7. doi: 10.1038/s41559-017-0158. Vis sammendrag

  Parallel evolution of similar traits by independent populations in similar environments is considered strong evidence for adaptation by natural selection. Often, however, replicate populations in similar environments do not all evolve in the same way, thus deviating from any single, predominant outcome of evolution. This variation might arise from non-adaptive, population-specific effects of genetic drift, gene flow or limited genetic variation. Alternatively, these deviations from parallel evolution might also reflect predictable adaptation to cryptic environmental heterogeneity within discrete habitat categories. Here, we show that deviations from parallel evolution are the consequence of environmental variation within habitats combined with variation in gene flow. Threespine stickleback (Gasterosteus aculeatus) in adjoining lake and stream habitats (a lake–stream ‘pair’) diverge phenotypically, yet the direction and magnitude of this divergence is not always fully parallel among 16 replicate pairs. We found that the multivariate direction of lake–stream morphological divergence was less parallel between pairs whose environmental differences were less parallel. Thus, environmental heterogeneity among lake–stream pairs contributes to deviations from parallel evolution. Additionally, likely genomic targets of selection were more parallel between environmentally more similar pairs. In contrast, variation in the magnitude of lake–stream divergence (independent of direction) was better explained by differences in lake–stream gene flow; pairs with greater lake–stream gene flow were less morphologically diverged. Thus, both adaptive and non-adaptive processes work concurrently to generate a continuum of parallel evolution across lake–stream stickleback population pairs.

• Ravinet, Mark Simon Paul; Faria, R; Butlin, RK; Galindo, J; Bierne, N & Rafajlovic, M [Vis alle 9 forfattere av denne artikkelen] (2017). Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. Journal of Evolutionary Biology. ISSN 1010-061X. 30(8), s. 1450–1477. doi: 10.1111/jeb.13047.
• Ishikawa, Asano; Kusakabe, Makoto; Yoshida, Kohta; Ravinet, Mark Simon Paul; Makino, Takashi & Toyoda, Atsushi [Vis alle 8 forfattere av denne artikkelen] (2017). Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. Evolution. ISSN 0014-3820. 71(3), s. 565–581. doi: 10.1111/evo.13175.
• Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Tørresen, Ole Kristian; Hagen, Ingerid; Lien, Sigbjørn & Nederbragt, Alexander Johan [Vis alle 9 forfattere av denne artikkelen] (2017). The genomic mosaicism of hybrid speciation. Science Advances. ISSN 2375-2548. 3, s. 1–16. doi: 10.1126/sciadv.1602996. Fulltekst i vitenarkiv
• Kusakabe, Makoto; Ishikawa, Asano; Ravinet, Mark Simon Paul; Yoshida, Kohta; Makino, Takashi & Toyoda, Atsushi [Vis alle 8 forfattere av denne artikkelen] (2017). Genetic basis for variation in salinity tolerance between stickleback ecotypes. Molecular Ecology. ISSN 0962-1083. 26(1), s. 304–319. doi: 10.1111/mec.13875.
• Fountain, Toby; Ravinet, Mark Simon Paul; Naylor, Richard; Reinhardt, Klaus & Butlin, Roger K. (2016). A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius. G3: Genes, Genomes, Genetics. ISSN 2160-1836. 6, s. 4059–4066. doi: 10.1534/g3.116.033092.
• Ravinet, Mark Simon Paul; Ishikawa, Asano & Kitano, Jun (2016). Trophic niche differentiation and phenotypic divergence among cryptic species of Japanese ninespine sticklebacks. Evolutionary Ecology Research. ISSN 1522-0613. 17(4), s. 505–523.

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• Sætre, Glenn-Peter & Ravinet, Mark (2019). Evolutionary Genetics: Concepts, Analysis, and Practice. Oxford University Press. ISBN 9780198830924. 336 s.

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• Hoff, Siv Nam Khang; Maurstad, Marius Filomeno; Alan, Le Moan; Ravinet, Mark; Durant, Joël & Tørresen, Ole K. [Vis alle 18 forfattere av denne artikkelen] (2023). Identification of multiple chromosomal inversions and fusions in a keystone Arctic species with high gene flow.
• Hoff, Siv Nam Khang; Maurstad, Marius Filomeno; Le Moan, Alan; Ravinet, Mark; Durant, Joël & Tørresen, Ole Kristian [Vis alle 18 forfattere av denne artikkelen] (2023). Identification of multiple chromosomal inversions and fusions in a keystone Arctic species with high gene flow.
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Vis alle 7 forfattere av denne artikkelen] (2023). Population genomics reveal multiple lineages with leaky intersterility barriers in the widespread forest fungus Trichaptum abietinum.
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Vis alle 7 forfattere av denne artikkelen] (2023). Understanding the nature of the reproductive barriers within the wood decay species Trichaptum abietinum.
• Kinneberg, Vilde Bruhn; Lü, Dabao Sun; Peris, David; Ravinet, Mark & Skrede, Inger (2022). Ancient introgression between highly divergent fungal sister species.
• Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; Maurice, Sundy; Kauserud, Håvard & Ravinet, Mark [Vis alle 7 forfattere av denne artikkelen] (2022). Understanding the nature of the reproductive barriers within the wood decay species Trichaptum abietinum.
• Lu, Dabao Sun; Skrede, Inger; Kauserud, Håvard; Navarro, David Peris; Maurice, Sandy & Ravinet, Mark [Vis alle 7 forfattere av denne artikkelen] (2020). Population genomics of Trichaptum abietinum - a window into fungal speciation.
• Lu, Dabao Sun; Skrede, Inger; Kauserud, Håvard; Navarro, David Peris; Sønstebø, Jørn Henrik & Maurice, Sandy [Vis alle 7 forfattere av denne artikkelen] (2020). Population genomics of Trichaptum abietinum - a window into fungal speciation.
• Westram, AM & Ravinet, Mark Simon Paul (2017). Land ahoy? Navigating the genomic landscape of speciation while avoiding shipwreck. Journal of Evolutionary Biology. ISSN 1010-061X. 30(8), s. 1522–1525. doi: 10.1111/jeb.13129.
• Ravinet, Mark Simon Paul (2016). Interpreting the genomic landscape of speciation: finding barriers to gene flow in genome scan data.
• Lü, Dabao Sun; Peris, David; Skrede, Inger; Kauserud, Håvard; Ravinet, Mark & Sønstebø, Jørn Henrik [Vis alle 8 forfattere av denne artikkelen] (2023). Fungi contain multitudes: Tempo and modes of evolution in the purplepore bracket fungus Trichaptum. University of Oslo. ISSN 1501-7710. Fulltekst i vitenarkiv

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