Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish.

التفاصيل البيبلوغرافية
العنوان:	Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish.
المؤلفون:	Schmid S; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Bachmann Salvy M; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Garcia Jimenez A; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Bertrand JAM; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Cortesi F; Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia.; School of the Environment, The University of Queensland, Brisbane, Queensland, Australia., Heim S; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Huyghe F; Marine Biology Laboratory, Department of Ecology and Biodiversity, Vrije Universiteit Brussel, Brussel, Belgium., Litsios G; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., Marcionetti A; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland., O'Donnell JL; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA., Riginos C; School of the Environment, The University of Queensland, Brisbane, Queensland, Australia., Tettamanti V; Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia., Salamin N; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
المصدر:	Molecular ecology [Mol Ecol] 2024 Jul; Vol. 33 (14), pp. e17436. Date of Electronic Publication: 2024 Jun 14.
نوع المنشور:	Journal Article
اللغة:	English
بيانات الدورية:	Publisher: Blackwell Scientific Publications Country of Publication: England NLM ID: 9214478 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-294X (Electronic) Linking ISSN: 09621083 NLM ISO Abbreviation: Mol Ecol Subsets: MEDLINE
أسماء مطبوعة:	Original Publication: Oxford, UK : Blackwell Scientific Publications, c1992-
مواضيع طبية MeSH:	Gene Flow* , Perciformes/genetics , Perciformes/classification , Genetics, Population*, Animals ; Pacific Ocean ; Pigmentation/genetics ; Indian Ocean ; Biological Evolution ; Whole Genome Sequencing ; Color
مستخلص:	Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm. (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)
References:	Alexa, A., & Rahnenfuhrer, J. (2020). topGO: Enrichment analysis for Gene Ontology. R package version 2.43.0. Allen, G. R. (2008). Conservation hotspots of biodiversity and endemism for Indo‐Pacific coral reef fishes. Aquatic Conservation: Marine and Freshwater Ecosystems, 18(5), 541–556. https://doi.org/10.1002/aqc.880. Allendorf, F. W., Hohenlohe, P. A., & Luikart, G. (2010). Genomics and the future of conservation genetics. Nature Reviews Genetics, 11(10), 697–709. https://doi.org/10.1038/nrg2844. Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Arroyo‐Correa, B., Jordano, P., & Bartomeus, I. (2023). Intraspecific variation in species interactions promotes the feasibility of mutualistic assemblages. Ecology Letters, 26(3), 448–459. https://doi.org/10.1111/ele.14163. Barabás, G., & D'Andrea, R. (2016). The effect of intraspecific variation and heritability on community pattern and robustness. Ecology Letters, 19(8), 977–986. https://doi.org/10.1111/ele.12636. Barber, P. H., Palumbi, S. R., Erdmann, M. V., & Moosa, M. K. (2000). A marine Wallace's line? Nature, 406(6797), 692–693. https://doi.org/10.1038/35021135. Barnett, D. W., Garrison, E. K., Quinlan, A. R., Strömberg, M. P., & Marth, G. T. (2011). BamTools: A C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691–1692. https://doi.org/10.1093/bioinformatics/btr174. Bay, L. K., & Caley, M. J. (2011). Greater genetic diversity in spatially restricted coral reef fishes suggests secondary contact among differentiated lineages. Diversity, 3(3), 483–502. https://doi.org/10.3390/d3030483. Belanger, C. L., Jablonski, D., Roy, K., Berke, S. K., Krug, A. Z., & Valentine, J. W. (2012). Global environmental predictors of benthic marine biogeographic structure. Proceedings of the National Academy of Sciences of the United States of America, 109(35), 14046–14051. https://doi.org/10.1073/pnas.1212381109. Beldade, R., Holbrook, S. J., Schmitt, R. J., Planes, S., Malone, D., & Bernardi, G. (2012). Larger female fish contribute disproportionately more to self‐replenishment. Proceedings of the Royal Society B: Biological Sciences, 279(1736), 2116–2121. https://doi.org/10.1098/rspb.2011.2433. Bell, L. J., Moyer, J. T., & Numachi, K. (1982). Morphological and genetic variation in Japanese populations of the anemonefish Amphiprion clarkii. Marine Biology, 72(2), 99–108. https://doi.org/10.1007/BF00396909. Belleghem, S. M. V., Rastas, P., Papanicolaou, A., Martin, S. H., Arias, C. F., Supple, M. A., Hanly, J. J., Mallet, J., Lewis, J. J., Hines, H. M., Ruiz, M., Salazar, C., Linares, M., Moreira, G. R. P., Jiggins, C. D., Counterman, B. A., McMillan, W. O., & Papa, R. (2017). Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology & Evolution, 1(3), 0052. https://doi.org/10.1038/s41559‐016‐0052. Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B: Methodological, 57(1), 289–300. https://doi.org/10.1111/j.2517‐6161.1995.tb02031.x. Briggs, J. C. (2003). Marine centres of origin as evolutionary engines. Journal of Biogeography, 30(1), 1–18. https://doi.org/10.1046/j.1365‐2699.2003.00810.x. Buckley, S. J., Brauer, C. J., Unmack, P. J., Hammer, M. P., & Beheregaray, L. B. (2022). Variation in intraspecific demography drives localised concordance but species‐wide discordance in response to past climatic change. BMC Ecology and Evolution, 22(1), 35. https://doi.org/10.1186/s12862‐022‐01990‐2. Burri, R., Nater, A., Kawakami, T., Mugal, C. F., Olason, P. I., Smeds, L., Suh, A., Dutoit, L., Bureš, S., Garamszegi, L. Z., Hogner, S., Moreno, J., Qvarnström, A., Ružić, M., Sæther, S.‐A., Sæthre, G.‐P., Török, J., & Ellegren, H. (2015). Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research, 25(11), 1656–1665. https://doi.org/10.1101/gr.196485.115. Buston, P. M., & García, M. B. (2007). An extraordinary life span estimate for the clown anemonefish Amphiprion percula. Journal of Fish Biology, 70(6), 1710–1719. https://doi.org/10.1111/j.1095‐8649.2007.01445.x. Buston, P. M., Jones, G. P., Planes, S., & Thorrold, S. R. (2012). Probability of successful larval dispersal declines fivefold over 1 km in a coral reef fish. Proceedings of the Royal Society B: Biological Sciences, 279(1735), 1883–1888. https://doi.org/10.1098/rspb.2011.2041. Cadena, C. D., & Zapata, F. (2021). The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked? Ornithology, 138(2), ukaa069. https://doi.org/10.1093/ornithology/ukaa069. Campagna, L., Repenning, M., Silveira, L. F., Fontana, C. S., Tubaro, P. L., & Lovette, I. J. (2017). Repeated divergent selection on pigmentation genes in a rapid finch radiation. Science Advances, 3(5), e1602404. https://doi.org/10.1126/sciadv.1602404. Canino, M. F., Spies, I. B., Cunningham, K. M., Hauser, L., & Grant, W. S. (2010). Multiple ice‐age refugia in Pacific cod, Gadus macrocephalus. Molecular Ecology, 19(19), 4339–4351. https://doi.org/10.1111/j.1365‐294X.2010.04815.x. Capblancq, T., & Forester, B. R. (2021). Redundancy analysis: A swiss army knife for landscape genomics. Methods in Ecology and Evolution, 12(12), 2298–2309. https://doi.org/10.1111/2041‐210X.13722. Capblancq, T., Mavárez, J., Rioux, D., & Després, L. (2019). Speciation with gene flow: Evidence from a complex of alpine butterflies (Coenonympha, Satyridae). Ecology and Evolution, 9(11), 6444–6457. https://doi.org/10.1002/ece3.5220. Choo, L. Q., Bal, T. M. P., Goetze, E., & Peijnenburg, K. T. C. A. (2021). Oceanic dispersal barriers in a holoplanktonic gastropod. Journal of Evolutionary Biology, 34(1), 224–240. https://doi.org/10.1111/jeb.13735. Clark, R. D., Aardema, M. L., Andolfatto, P., Barber, P. H., Hattori, A., Hoey, J. A., Montes, H. R., & Pinsky, M. L. (2021). Genomic signatures of spatially divergent selection at clownfish range margins. Proceedings of the Royal Society B: Biological Sciences, 288(1952), 20210407. https://doi.org/10.1098/rspb.2021.0407. Comerford, M., & Egan, S. P. (2022). The potential role of spatial sorting in speciation and adaptive radiations. Population Ecology, 2022, 1–8. https://doi.org/10.1002/1438‐390X.12108. Conover, D. O., Clarke, L. M., Munch, S. B., & Wagner, G. N. (2006). Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation. Journal of Fish Biology, 69(sc), 21–47. https://doi.org/10.1111/j.1095‐8649.2006.01274.x. Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology, 23(13), 3133–3157. https://doi.org/10.1111/mec.12796. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330. De Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56(6), 879–886. https://doi.org/10.1080/10635150701701083. Delrieu‐Trottin, E., Mona, S., Maynard, J., Neglia, V., Veuille, M., & Planes, S. (2017). Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Scientific Reports, 7(1), 40,519. https://doi.org/10.1038/srep40519. Devi, V. S., Salitha, S., Jose, S., Paramasivam, P., Anand, J., Ajith, K. T. T., & Kuldeep, K. L. (2021). Molecular characterization on the morphotypes of Amphiprion clarkii (Bennett, 1830) from Indian waters with biogeographic notes. Thalassas: An International Journal of Marine Sciences, 37, 477–485. https://doi.org/10.1007/s41208‐021‐00330‐3. Dohna, T. A., Timm, J., Hamid, L., & Kochzius, M. (2015). Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo‐Malay archipelago: Inferences from a mitochondrial and microsatellite loci. Ecology and Evolution, 5(8), 1717–1733. https://doi.org/10.1002/ece3.1455. Drew, J., & Barber, P. H. (2009). Sequential cladogenesis of the reef fish Pomacentrus moluccensis (Pomacentridae) supports the peripheral origin of marine biodiversity in the Indo‐Australian archipelago. Molecular Phylogenetics and Evolution, 53(1), 335–339. https://doi.org/10.1016/j.ympev.2009.04.014. Duftner, N., Sefc, K. M., Koblmüller, S., Salzburger, W., Taborsky, M., & Sturmbauer, C. (2007). Parallel evolution of facial stripe patterns in the Neolamprologus brichardi/pulcher species complex endemic to Lake Tanganyika. Molecular Phylogenetics and Evolution, 45(2), 706–715. https://doi.org/10.1016/j.ympev.2007.08.001. Edelman, N. B., Frandsen, P. B., Miyagi, M., Clavijo, B., Davey, J., Dikow, R. B., García‐Accinelli, G., Belleghem, S. M. V., Patterson, N., Neafsey, D. E., Challis, R., Kumar, S., Moreira, G. R. P., Salazar, C., Chouteau, M., Counterman, B. A., Papa, R., Blaxter, M., Reed, R. D., … Mallet, J. (2019). Genomic architecture and introgression shape a butterfly radiation. Science, 366(6465), 594–599. https://doi.org/10.1126/science.aaw2090. Ellegren, H. (2014). Genome sequencing and population genomics in non‐model organisms. Trends in Ecology & Evolution, 29(1), 51–63. https://doi.org/10.1016/j.tree.2013.09.008. Endler, J. A. (2012). A framework for analysing colour pattern geometry: Adjacent colours. Biological Journal of the Linnean Society, 107(2), 233–253. https://doi.org/10.1111/j.1095‐8312.2012.01937.x. Excoffier, L., Dupanloup, I., Huerta‐Sánchez, E., Sousa, V. C., & Foll, M. (2013). Robust demographic inference from genomic and SNP data. PLoS Genetics, 9(10), e1003905. https://doi.org/10.1371/journal.pgen.1003905. Fautin, D. G., & Allen, G. R. (1997). Field guide to anemonefishes and their host sea anemones (2nd revised ed.) ed. Western Australian Museum. Fitzpatrick, J. M., Carlon, D. B., Lippe, C., & Robertson, D. R. (2011). The West Pacific diversity hotspot as a source or sink for new species? Population genetic insights from the Indo‐Pacific parrotfish Scarus rubroviolaceus. Molecular Ecology, 20(2), 219–234. https://doi.org/10.1111/j.1365‐294X.2010.04942.x. Fleminger, A. (1986). The Pleistocene equatorial barrier between the Indian and Pacific oceans and a likely cause for Wallace's line. UNESCO Technical Papers in Marine Science, 49, 84–97. Forsman, A., Ahnesjö, J., Caesar, S., & Karlsson, M. (2008). A model of ecological and evolutionary consequences of color polymorphism. Ecology, 89(1), 34–40. https://doi.org/10.1890/07‐0572.1. Frédérich, B., Liu, S.‐Y. V., & Dai, C.‐F. (2012). Morphological and genetic divergences in a coral reef damselfish, Pomacentrus coelestis. Evolutionary Biology, 39(3), 359–370. https://doi.org/10.1007/s11692‐011‐9158‐z. Gaboriau, T., Leprieur, F., Mouillot, D., & Hubert, N. (2017). Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo‐Pacific. Ecography, 41(8), 1295–1306. https://doi.org/10.1111/ecog.02589. Gainsford, A., Jones, G. P., Hobbs, J. A., Heindler, F. M., & Herwerden, L. (2020). Species integrity, introgression, and genetic variation across a coral reef fish hybrid zone. Ecology and Evolution, 10(21), 11998–12014. https://doi.org/10.1002/ece3.6769. Gaither, M. R., Toonen, R. J., Robertson, D. R., Planes, S., & Bowen, B. W. (2010). Genetic evaluation of marine biogeographical barriers: Perspectives from two widespread Indo‐Pacific snappers (Lutjanus kasmira and Lutjanus fulvus). Journal of Biogeography, 37(1), 133–147. https://doi.org/10.1111/j.1365‐2699.2009.02188.x. Gandra, M., Assis, J., Martins, M. R., & Abecasis, D. (2021). Reduced global genetic differentiation of exploited marine fish species. Molecular Biology and Evolution, 38(4), 1402–1412. https://doi.org/10.1093/molbev/msaa299. Glémin, S., Ronfort, J., & Bataillon, T. (2003). Patterns of inbreeding depression and architecture of the load in subdivided populations. Genetics, 165(4), 2193–2212. https://doi.org/10.1093/genetics/165.4.2193. Gray, S. M., & McKinnon, J. S. (2007). Linking color polymorphism maintenance and speciation. Trends in Ecology & Evolution, 22(2), 71–79. https://doi.org/10.1016/j.tree.2006.10.005. Hartasánchez, D. A., Vallès‐Codina, O., Brasó‐Vives, M., & Navarro, A. (2014). Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario. G3: Genes, Genomes, Genetics, 4(8), 1479–1489. https://doi.org/10.1534/g3.114.012435. Hellberg, M. E. (2009). Gene flow and isolation among populations of marine animals. Annual Review of Ecology, Evolution, and Systematics, 40(1), 291–310. https://doi.org/10.1146/annurev.ecolsys.110308.120223. Hench, K., Helmkampf, M., McMillan, W. O., & Puebla, O. (2022). Rapid radiation in a highly diverse marine environment. Proceedings of the National Academy of Sciences, 119(4), e2020457119. https://doi.org/10.1073/pnas.2020457119. Hewitt, G. (2000). The genetic legacy of the quaternary ice ages. Nature, 405(6789), 907–913. https://doi.org/10.1038/35016000. Hoeksema, B. W. (2007). Delineation of the Indo‐Malayan Centre of maximum marine biodiversity: The coral triangle. In W. Renema (Ed.), Biogeography, time, and place: Distributions, barriers, and islands (pp. 117–178). Springer Netherlands. https://doi.org/10.1007/978‐1‐4020‐6374‐9_5. Horne, J. B., van Herwerden, L., Choat, J. H., & Robertson, D. R. (2008). High population connectivity across the Indo‐Pacific: Congruent lack of phylogeographic structure in three reef fish congeners. Molecular Phylogenetics and Evolution, 49(2), 629–638. https://doi.org/10.1016/j.ympev.2008.08.023. Hugall, A. F., & Stuart‐Fox, D. (2012). Accelerated speciation in colour‐polymorphic birds. Nature, 485(7400), 631–634. https://doi.org/10.1038/nature11050. Hughes, T. P., Bellwood, D. R., & Connolly, S. R. (2002). Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecology Letters, 5(6), 775–784. https://doi.org/10.1046/j.1461‐0248.2002.00383.x. Huyghe, F., & Kochzius, M. (2017). Highly restricted gene flow between disjunct populations of the skunk clownfish (Amphiprion akallopisos) in the Indian Ocean. Marine Ecology, 38(1), e12357. https://doi.org/10.1111/maec.12357. Huyghe, F., & Kochzius, M. (2018). Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian ocean. PLoS One, 13(3), e0193825. https://doi.org/10.1371/journal.pone.0193825. Jones, G. P., Planes, S., & Thorrold, S. R. (2005). Coral reef fish larvae settle close to home. Current Biology, 15(14), 1314–1318. https://doi.org/10.1016/j.cub.2005.06.061. Joshi, N., & Fass, J. (2011). Sickle: A sliding‐window, adaptive, quality‐based trimming tool for FastQ files. https://github.com/najoshi/sickle. Kawecki, T. J. (2008). Adaptation to marginal habitats. Annual Review of Ecology, Evolution, and Systematics, 39(1), 321–342. https://doi.org/10.1146/annurev.ecolsys.38.091206.095622. Keyse, J., Crandall, E. D., Toonen, R. J., Meyer, C. P., Treml, E. A., & Riginos, C. (2014). The scope of published population genetic data for Indo‐Pacific marine fauna and future research opportunities in the region. Bulletin of Marine Science, 90, 47–78. https://doi.org/10.5343/bms.2012.1107. Kool, J. T., Paris, C. B., Barber, P. H., & Cowen, R. K. (2011). Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities. Global Ecology and Biogeography, 20(5), 695–706. https://doi.org/10.1111/j.1466‐8238.2010.00637.x. Legendre, P., & Legendre, L. (1998). Numerical ecology. Elsevier. Lehmann, R., Lightfoot, D. J., Schunter, C., Michell, C. T., Ohyanagi, H., Mineta, K., Foret, S., Berumen, M., Miller, D. J., Aranda, M., Gojobori, T., Munday, P. L., & Ravasi, T. (2018). Finding Nemo's genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula. Molecular Ecology Resources, 19(3), 570–585. https://doi.org/10.1101/278267. Lessios, H. A., Kane, J., & Robertson, D. R. (2003). Phylogeography of the pantropical sea urchin Tripneustes: Contrasting patterns of population structure between oceans. Evolution, 57(9), 2026–2036. https://doi.org/10.1111/j.0014‐3820.2003.tb00382.x. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352. Link, V., Kousathanas, A., Veeramah, K., Sell, C., Scheu, A., & Wegmann, D. (2017). ATLAS: Analysis tools for low‐depth and ancient Samples. BioRxiv. https://doi.org/10.1101/105346. Litsios, G., Kostikova, A., & Salamin, N. (2014). Host specialist clownfishes are environmental niche generalists. Proceedings of the Royal Society of London B: Biological Sciences, 281(1795), 20133220. https://doi.org/10.1098/rspb.2013.3220. Litsios, G., Pearman, P. B., Lanterbecq, D., Tolou, N., & Salamin, N. (2014). The radiation of the clownfishes has two geographical replicates. Journal of Biogeography, 41(11), 2140–2149. https://doi.org/10.1111/jbi.12370. Litsios, G., & Salamin, N. (2014). Hybridisation and diversification in the adaptive radiation of clownfishes. BMC Evolutionary Biology, 14(1), 245. https://doi.org/10.1186/s12862‐014‐0245‐5. Litsios, G., Sims, C. A., Wüest, R. O., Pearman, P. B., Zimmermann, N. E., & Salamin, N. (2012). Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology, 12(1), 212. https://doi.org/10.1186/1471‐2148‐12‐212. Liu, M., Lin, L., Gao, T., Yanagimoto, T., Sakurai, Y., & Grant, W. S. (2012). What maintains the central North Pacific genetic discontinuity in Pacific herring? PLoS One, 7(12), e50340. https://doi.org/10.1371/journal.pone.0050340. Liu, S.‐Y. V., Chang, F.‐T., Borsa, P., Chen, W.‐J., & Dai, C.‐F. (2014). Phylogeography of the humbug damselfish, Dascyllus aruanus (Linnaeus, 1758): Evidence of Indo‐Pacific vicariance and genetic differentiation of peripheral populations. Biological Journal of the Linnean Society, 113(4), 931–942. https://doi.org/10.1111/bij.12378. Liu, S. Y. V., Tuanmu, M.‐N., Rachmawati, R., Mahardika, G. N., & Barber, P. H. (2019). Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis). PeerJ, 7, e7384. https://doi.org/10.7717/peerj.7384. Lohman, D. J., De Bruyn, M., Page, T., Von Rintelen, K., Hall, R., Ng, P. K. L., Shih, H.‐T., Carvalho, G. R., & Von Rintelen, T. (2011). Biogeography of the Indo‐Australian archipelago. Annual Review of Ecology, Evolution, and Systematics, 42(1), 205–226. https://doi.org/10.1146/annurev‐ecolsys‐102,710‐145,001. Lorin, T., Brunet, F. G., Laudet, V., & Volff, J.‐N. (2018). Teleost fish‐specific preferential retention of pigmentation gene‐containing families after whole genome duplications in vertebrates. G3: Genes, Genomes, Genetics, 8(5), 1795–1806. https://doi.org/10.1534/g3.118.200201. Madduppa, H. H., Timm, J., & Kochzius, M. (2014). Interspecific, spatial and temporal variability of self‐recruitment in anemonefishes. PLoS One, 9(2), e90648. https://doi.org/10.1371/journal.pone.0090648. Malinsky, M., Challis, R. J., Tyers, A. M., Schiffels, S., Terai, Y., Ngatunga, B. P., Miska, E. A., Durbin, R., Genner, M. J., & Turner, G. F. (2015). Genomic islands of speciation separate cichlid ecomorphs in an east African crater lake. Science, 350(6267), 1493–1498. https://doi.org/10.1126/science.aac9927. Marcionetti, A. (2021). Genomics of clownfish adaptive radiation. University of Lausanne. Marcionetti, A., Bertrand, J. A. M., Cortesi, F., Donati, G. F. A., Heim, S., Huyghe, F., Kochzius, M., Pellissier, L., & Salamin, N. (2024). Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Molecular Ecology, 33(11), e17347. https://doi.org/10.1111/mec.17347. Marcionetti, A., Rossier, V., Roux, N., Salis, P., Laudet, V., & Salamin, N. (2019). Insights into the genomics of clownfish adaptive radiation: Genetic basis of the mutualism with sea anemones. Genome Biology and Evolution, 11(3), 869–882. https://doi.org/10.1093/gbe/evz042. Marcionetti, A., & Salamin, N. (2023). Insights into the genomics of clownfish adaptive radiation: The genomic substrate of the diversification. Genome Biology and Evolution, 15(7), evad088. https://doi.org/10.1093/gbe/evad088. Marko, P. B. (2004). “What's larvae got to do with it?” Disparate patterns of post‐glacial population structure in two benthic marine gastropods with identical dispersal potential. Molecular Ecology, 13(3), 597–611. https://doi.org/10.1046/j.1365‐294x.2004.02096.x. Marques, D. A., Meier, J. I., & Seehausen, O. (2019). A combinatorial view on speciation and adaptive radiation. Trends in Ecology & Evolution, 34(6), 531–544. https://doi.org/10.1016/j.tree.2019.02.008. Martin, M. (2011). Cutadapt removes adapter sequences from high‐throughput sequencing reads. EMBnet. Journal, 17(1), 10–12. https://doi.org/10.14806/ej.17.1.200. Meisner, J., & Albrechtsen, A. (2018). Inferring population structure and admixture proportions in low‐depth NGS data. Genetics, 210(2), 719–731. https://doi.org/10.1534/genetics.118.301336. Messer, P. W., Ellner, S. P., & Hairston, N. G. (2016). Can population genetics adapt to rapid evolution? Trends in Genetics, 32(7), 408–418. https://doi.org/10.1016/j.tig.2016.04.005. Meyer, A. (2006). Repeating patterns of mimicry. PLoS Biology, 4(10), e341. https://doi.org/10.1371/journal.pbio.0040341. Meyer, C. P., Geller, J. B., & Paulay, G. (2005). Fine scale endemism on coral reefs: Archipelagic differentiation in turbinid gastropods. Evolution, 59(1), 113–125. https://doi.org/10.1111/j.0014‐3820.2005.tb00899.x. Militz, T. A., McCormick, M. I., Schoeman, D. S., Kinch, J., & Southgate, P. C. (2016). Frequency and distribution of melanistic morphs in coexisting population of nine clownfish species in Papua New Guinea. Marine Biology, 163(10), 200. https://doi.org/10.1007/s00227‐016‐2972‐1. Nikolic, N., Liu, S., Jacobsen, M. W., Jónsson, B., Bernatchez, L., Gagnaire, P.‐A., & Hansen, M. M. (2020). Speciation history of European (Anguilla Anguilla) and American eel (A. rostrata), analysed using genomic data. Molecular Ecology, 29(3), 565–577. https://doi.org/10.1111/mec.15342. Noor, M. A. F., & Bennett, S. M. (2009). Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity, 103(6), 439–444. https://doi.org/10.1038/hdy.2009.151. Oleksiak, M. F. (2019). Adaptation without boundaries: Population genomics in marine systems. In O. P. Rajora (Ed.), Population genomics: Concepts, approaches and applications (pp. 587–612). Springer International Publishing. https://doi.org/10.1007/13836_2018_32. Ollerton, J., McCollin, D., Fautin, D. G., & Allen, G. R. (2007). Finding NEMO: Nestedness engendered by mutualistic organization in anemonefish and their hosts. Proceedings of the Royal Society of London B: Biological Sciences, 274(1609), 591–598. https://doi.org/10.1098/rspb.2006.3758. Ortego, J., Gugger, P. F., & Sork, V. L. (2018). Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). New Phytologist, 218(2), 804–818. https://doi.org/10.1111/nph.14951. Palumbi, S. R. (1992). Marine speciation on a small planet. Trends in Ecology & Evolution, 7(4), 114–118. https://doi.org/10.1016/0169‐5347(92)90144‐Z. Pease, J. B., & Hahn, M. W. (2013). More accurate phylogenies inferred from low‐recombination regions in the presence of incomplete lineage sorting. Evolution; International Journal of Organic Evolution, 67(8), 2376–2384. https://doi.org/10.1111/evo.12118. Pellissier, L., Leprieur, F., Parravicini, V., Cowman, P. F., Kulbicki, M., Litsios, G., Olsen, S. M., Wisz, M. S., Bellwood, D. R., & Mouillot, D. (2014). Quaternary coral reef refugia preserved fish diversity. Science, 344(6187), 1016–1019. https://doi.org/10.1126/science.1249853. Petzold, A., & Hassanin, A. (2020). A comparative approach for species delimitation based on multiple methods of multi‐locus DNA sequence analysis: A case study of the genus Giraffa (Mammalia, Cetartiodactyla). PLoS One, 15(2), e0217956. https://doi.org/10.1371/journal.pone.0217956. Pinsky, M. L., Montes, H. R., & Palumbi, S. R. (2010). Using isolation by distance and effective density to estimate dispersal scales in anemonefish. Evolution; International Journal of Organic Evolution, 64(9), 2688–2700. https://doi.org/10.1111/j.1558‐5646.2010.01003.x. Renema, W., Bellwood, D. R., Braga, J. C., Bromfield, K., Hall, R., Johnson, K. G., Lunt, P., Meyer, C. P., McMonagle, L. B., Morley, R. J., O'Dea, A., Todd, J. A., Wesselingh, F. P., Wilson, M. E. J., & Pandolfi, J. M. (2008). Hopping hotspots: Global shifts in marine biodiversity. Science, 321(5889), 654–657. https://doi.org/10.1126/science.1155674. Rolland, J., Silvestro, D., Litsios, G., Faye, L., & Salamin, N. (2018). Clownfishes evolution below and above the species level. Proceedings of the Royal Society B: Biological Sciences, 285(1873), 20171796. https://doi.org/10.1098/rspb.2017.1796. Roux, N., Salis, P., Lambert, A., Logeux, V., Soulat, O., Romans, P., Frédérich, B., Lecchini, D., & Laudet, V. (2019). Staging and normal table of postembryonic development of the clownfish (Amphiprion ocellaris). Developmental Dynamics: An Official Publication of the American Association of the Anatomists, 248(7), 545–568. https://doi.org/10.1002/dvdy.46. Roux, N., Salis, P., Lee, S.‐H., Besseau, L., & Laudet, V. (2020). Anemonefish, a model for eco‐Evo‐devo. EvoDevo, 11, 20. https://doi.org/10.1186/s13227‐020‐00166‐7. Rudman, S. M., Rodriguez‐Cabal, M. A., Stier, A., Sato, T., Heavyside, J., El‐Sabaawi, R. W., & Crutsinger, G. M. (2015). Adaptive genetic variation mediates bottom‐up and top‐down control in an aquatic ecosystem. Proceedings of the Royal Society B: Biological Sciences, 282(1812), 20151234. https://doi.org/10.1098/rspb.2015.1234. Salinas‐de‐León, P., Jones, T., & Bell, J. J. (2012). Successful determination of larval dispersal distances and subsequent settlement for long‐lived pelagic larvae. PLoS One, 7(3), e32788. https://doi.org/10.1371/journal.pone.0032788. Santini, S., & Polacco, G. (2006). Finding Nemo: Molecular phylogeny and evolution of the unusual life style of anemonefish. Gene, 385, 19–27. https://doi.org/10.1016/j.gene.2006.03.028. Schindelin, J., Arganda‐Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.‐Y., White, D. J., Hartenstein, V., Eliceiri, K., Tomancak, P., & Cardona, A. (2012). Fiji: An open‐source platform for biological‐image analysis. Nature Methods, 9(7), 676–682. https://doi.org/10.1038/nmeth.2019. Schlager, S. (2017). Chapter 9 – Morpho and Rvcg – Shape analysis in R: R‐packages for geometric morphometrics, shape analysis and surface manipulations. In G. Zheng, S. Li, & G. Székely (Eds.), Statistical shape and deformation analysis (pp. 217–256). Academic Press. https://doi.org/10.1016/B978‐0‐12‐810,493‐4.00011‐0. Schmid, S., Bachmann Salvy, M., Garcia Jimenez, A., Bertrand, J. A. M., Cortesi, F., Heim, S., Huyghe, F., Litsios, G., Marcionetti, A., O'Donnell, J., Riginos, C., Tettamanti, V., & Salamin, N. (2023). Amphiprion clarkii population genomics. Genomic Observatories MetaDatabase (GEOME). https://n2t.net/ark:/21547/FbA2. Schmid, S., Micheli, B., Cortesi, F., Donati, G. F. A., & Salamin, N. (2022). Extensive hybridisation throughout clownfishes evolutionary history. bioRxiv. https://doi.org/10.1101/2022.07.08.499304. Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G., & Przeworski, M. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360(6389), 656–660. https://doi.org/10.1126/science.aar3684. Shanks, A. L., Grantham, B. A., & Carr, M. H. (2003). Propagule dispersal distance and the size and spacing of marine reserves. Ecological Applications, 13(sp1), 159–169. https://doi.org/10.1890/1051‐0761(2003)013[0159:PDDATS]2.0.CO;2. Shine, R., Brown, G. P., & Phillips, B. L. (2011). An evolutionary process that assembles phenotypes through space rather than through time. Proceedings of the National Academy of Sciences, 108(14), 5708–5711. https://doi.org/10.1073/pnas.1018989108. Simpson, S. D., Harrison, H. B., Claereboudt, M. R., & Planes, S. (2014). Long‐distance dispersal via ocean currents connects omani clownfish populations throughout entire species range. PLoS One, 9(9), e107610. https://doi.org/10.1371/journal.pone.0107610. Singhal, S., Hoskin, C. J., Couper, P., Potter, S., & Moritz, C. (2018). A framework for resolving cryptic species: A case study from the lizards of the Australian wet tropics. Systematic Biology, 67(6), 1061–1075. https://doi.org/10.1093/sysbio/syy026. Sirkia, P. M., & Qvarnstrom, A. (2021). Adaptive coloration in pied flycatchers (Ficedula hypoleuca)‐the devil is in the detail. Ecology and Evolution, 11(4), 1501–1525. https://doi.org/10.1002/ece3.7048. Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A. (2019). Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PLoS Biology, 17(7), e3000391. https://doi.org/10.1371/journal.pbio.3000391. Stryjewski, K. F., & Sorenson, M. D. (2017). Mosaic genome evolution in a recent and rapid avian radiation. Nature Ecology & Evolution, 1(12), 1912. https://doi.org/10.1038/s41559‐017‐0364‐7. Thresher, R. E., Colin, P. L., & Bell, L. J. (1989). Planktonic duration, distribution and population structure of western and central Pacific damselfishes (Pomacentridae). Copeia, 1989(2), 420–434. https://doi.org/10.2307/1445439. Timm, J., Planes, S., & Kochzius, M. (2012). High similarity of genetic population structure in the false clown anemonefish (Amphiprion ocellaris) found in microsatellite and mitochondrial control region analysis. Conservation Genetics, 13(3), 693–706. https://doi.org/10.1007/s10592‐012‐0318‐1. Toole, J. M., Millard, R. C., Wang, Z., & Pu, S. (1990). Observations of the Pacific north equatorial current bifurcation at the Philippine coast. Journal of Physical Oceanography, 20(2), 307–318. https://doi.org/10.1175/1520‐0485(1990)020<0307:OOTPNE>2.0.CO;2. Turner, T. L., Hahn, M. W., & Nuzhdin, S. V. (2005). Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3(9), e285. https://doi.org/10.1371/journal.pbio.0030285. Van Belleghem, S. M., Papa, R., Ortiz‐Zuazaga, H., Hendrickx, F., Jiggins, C. D., Owen McMillan, W., & Counterman, B. A. (2018). Patternize: An R package for quantifying colour pattern variation. Methods in Ecology and Evolution, 9(2), 390–398. https://doi.org/10.1111/2041‐210X.12853. Van der Ven, R. M., Flot, J.‐F., Buitrago‐López, C., & Kochzius, M. (2021). Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean. Heredity, 126(2), 351–365. https://doi.org/10.1038/s41437‐020‐00379‐5. Vaux, F., Bohn, S., Hyde, J. R., & O'Malley, K. G. (2021). Adaptive markers distinguish north and South Pacific albacore amid low population differentiation. Evolutionary Applications, 14(5), 1343–1364. https://doi.org/10.1111/eva.13202. Voris, H. K. (2000). Maps of Pleistocene sea levels in Southeast Asia: Shorelines, river systems and time durations. Journal of Biogeography, 27(5), 1153–1167. https://doi.org/10.1046/j.1365‐2699.2000.00489.x. Wang, N., Liang, B., Wang, J., Yeh, C.‐F., Liu, Y., Liu, Y., Liang, W., Yao, C.‐T., & Li, S.‐H. (2016). Incipient speciation with gene flow on a continental Island: Species delimitation of the Hainan hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves). Molecular Phylogenetics and Evolution, 102, 62–73. https://doi.org/10.1016/j.ympev.2016.05.022. Waples, R. S. (1998). Separating the wheat from the chaff: Patterns of genetic differentiation in high gene flow species. Journal of Heredity, 89(5), 438–450. https://doi.org/10.1093/jhered/89.5.438. Wellington, G. M., & Victor, B. C. (1989). Planktonic larval duration of one hundred species of Pacific and Atlantic damselfishes (Pomacentridae). Marine Biology, 101(4), 557–567. https://doi.org/10.1007/BF00541659. White, C., Selkoe, K. A., Watson, J., Siegel, D. A., Zacherl, D. C., & Toonen, R. J. (2010). Ocean currents help explain population genetic structure. Proceedings of the Royal Society B: Biological Sciences, 277(1688), 1685–1694. https://doi.org/10.1098/rspb.2009.2214. Winters, K. L., van Herwerden, L., Choat, J. H., & Robertson, D. R. (2010). Phylogeography of the Indo‐Pacific parrotfish Scarus psittacus: Isolation generates distinctive peripheral populations in two oceans. Marine Biology, 157(8), 1679–1691. https://doi.org/10.1007/s00227‐010‐1442‐4. Wolf, J. B. W., & Ellegren, H. (2017). Making sense of genomic islands of differentiation in light of speciation. Nature Reviews Genetics, 18(2), 87. https://doi.org/10.1038/nrg.2016.133. Wood, C. W., & Brodie, E. D. (2016). Evolutionary response when selection and genetic variation covary across environments. Ecology Letters, 19(10), 1189–1200. https://doi.org/10.1111/ele.12662. Ye, L., Yang, S.‐Y., Zhu, X.‐M., Liu, M., Lin, J.‐Y., & Wu, K.‐C. (2011). Effects of temperature on survival, development, growth and feeding of larvae of yellowtail clownfish Amphiprion clarkii (Pisces: Perciformes). Acta Ecologica Sinica, 31(5), 241–245. https://doi.org/10.1016/j.chnaes.2011.06.003.
معلومات مُعتمدة:	31003A-163428 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; DE200100620 Australian Research Council; DP180102363 Australian Research Council
فهرسة مساهمة:	Keywords: fish; genomics/proteomics; phylogeography; population genetics‐empirical
تواريخ الأحداث:	Date Created: 20240614 Date Completed: 20240708 Latest Revision: 20240708
رمز التحديث:	20240708
DOI:	10.1111/mec.17436
PMID:	38872589
قاعدة البيانات:	MEDLINE

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تدمد:	1365-294X
DOI:	10.1111/mec.17436