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Cochlearia) with Emphasis on Icelandic Populations Genetic structure of diploid (2n = 12, 14) Scurvygrasses (Cochlearia) with emphasis on Icelandic populations Luka Natassja Olsen MSc Thesis Centre for Ecology and Evolutionary Synthesis, Department of Biosciences UNIVERSITY OF OSLO September 2015 1 © Luka Natassja Olsen 2015 Genetic structure of diploid (2n = 12, 14) Scurvygrasses (Cochlearia) with emphasis on Icelandic populations Luka N. Olsen http://www.duo.uio.no/ Cover art: Sondre Strøm Linde Print: University Print Central, University of Oslo 2 Spoonwort doth warm, and also doth dry, In the Scurvy 'tis a great Remedy, It sends out all corrupt humors by sweat With this your mouth gargel often, and wet. This plant which deserves so much of your praise The Apothecaries use six several wayes, It's Spirit, Syrup, Water procures health, So doth its Salt conserve, and the Herb itself. 'Six several ways' (of using the treasured Spoonwort (Cochlearia) as a remedy of scurvy), as cited by Lorenz (1953) 3 4 Forord En stor takk til min hovedveileder Anne, for møter med kaffe, te og klemmer. Takk for laboratoriehjelp og utregninger, takk for utallige rettinger og tilbakemeldinger på utkast, og for svar på en myriade av spørsmål. Takk til medveileder Inger, for all nomenklaturisk og taksonomisk eksperthjelp i Cochlearia-feltet. I tillegg, takk for at du ble med Anne og meg ut i felt på Island som vår private sjåfør – til tross for at det skulle vise seg å innebære risikable turer over hraun for å krafse Cochlearia ut av klippesprekker! Takk til medveileder Charlotte, for at du hjalp til med gamle Islandske floraer på Tøyen. Takk til Marie, for at du viste vei for meg innenfor RAD-seq, STACKS og alt! Jeg er glad vi rakk å bli kjent før du ble ferdig med din oppgave. Takk til resten av Annes gruppe også, for koselige tirsdagsmøter. Takk til Sigríður og Ingrid Johansen, for at dere oversatte gamle Islandske floraer for meg. Takk til Paul Grini, for at du tok deg tid til å diskutere epigenetikk. Thank you, Robin, for all your thoughts, and for pushing me into trying bioinformatic gymnastics. Thank you, Annie, for feedback on my writing. Many thanks to Terezie Mandáková and Martin Lysák, for letting me stay in Brno. And to Terezie especially, for all help with the chromosome counts, both at the Mazaryk University in Czeck Republik, and here at UiO. En spesielt stor takk til Stine, Tonje og Mathilde, for at jeg fikk være en brøkdel av den fantastiske firkløveren vår. Det er usikkert om jeg ville likt meg så godt gjennom studiene om det ikke hadde vært for dere. Nå som den dårlige studentsamvittigheten omsider fordufter håper jeg at vi kan finne på noe utenfor lesesalen igjen. Takk også, til alle de fine samboerne mine, Åsa, Sverre, Veronika og Linnea, for at det ofte har vært klemmer å få og middag i kjøleskapet når jeg kommer sent hjem. Takk til familien min, spesielt Ronja, for alle oppmuntrende ord, og for at du tvinger meg til å ta kaffepauser selv når jeg tror jeg ikke trenger det. Sist, men ikke minst, takk til Sondre, for at du laget forside for meg, og for at du alltid synes jeg er den flinkeste i verden – uansett hva det er jeg foretar meg. 5 6 Index Abstract ...................................................................................................................................... 9 1 Introduction ...................................................................................................................... 11 1.1 Taxonomical treatment of Cochlearia in Iceland....................................................... 13 1.2 Research aims and questions ..................................................................................... 15 2 Materials and methods ..................................................................................................... 16 2.1 Plant material ............................................................................................................. 16 2.2 Chromosome counting ............................................................................................... 17 2.3 Morphometry ............................................................................................................. 19 2.4 DNA extraction .......................................................................................................... 21 2.5 RAD-sequencing ....................................................................................................... 21 Processing the raw RAD-seq reads .................................................................................. 23 Population structure analysis ............................................................................................ 25 Tree and network analyses ............................................................................................... 25 PCA analyses .................................................................................................................... 26 Maps ................................................................................................................................. 26 3 Results .............................................................................................................................. 27 3.1 Chromosome counting ............................................................................................... 27 3.2 Morphometry ............................................................................................................. 28 3.3 RAD-sequencing ....................................................................................................... 32 Population structure analysis ............................................................................................ 32 Tree and network analysis ................................................................................................ 33 Bayesian phylogeny ......................................................................................................... 35 PCA analysis .................................................................................................................... 36 4 Discussion ........................................................................................................................ 39 4.1 Do Icelandic plants with different chromosome number or ecology constitute different genetic clusters? ..................................................................................................... 39 4.2 How is the evolutionary relationship between the Icelandic plants and other diploid Cochlearia species? .............................................................................................................. 43 4.3 How can the results from this study be guiding for taxonomical decisions in Flora Nordica? ............................................................................................................................... 44 References ................................................................................................................................ 47 Appendix .................................................................................................................................. 52 7 8 Abstract Section Cochlearia (Brassicaceae) includes highly polymorphic species complexes with regard to ploidal level, ecological adaptation and distribution. Low levels of chloroplast DNA divergence suggest that taxa most likely have diversified relatively recently, and that speciation is still ongoing. This has led to conflicting taxonomic treatments. The European Cochlearia displays a range of ploidal levels, from diploid to decaploid. Diploid species with chromosome number 2n = 12 dominate in southwestern Europe, whereas the arctic Cochlearia is diploid with 2n = 14. In Iceland, diploid plants of both basic numbers (2n =12, 14) are found. Whereas the 2n = 12 plants are found only in beach cliffs along the Icelandic coast, the 2n = 14 plants are found in two different habitats: In snowbeds on inland mountains, and along the western coast of Iceland. There is still no agreement as to which taxa the Icelandic plants belong. It has been suggested that the 2n = 14 plants belong either to the arctic diploid C. groenlandica (2n = 14) or constitute a subspecies of the tetraploid C. officinalis (2n = 24). The 2n = 12 plants have been related either to C. groenlandica or to the southwestern European diploid C. pyrenaica (2n = 12). In this study, single nucleotide polymorphisms (SNPs) derived from RAD-sequencing were applied to study whether the Icelandic Cochlearia plants constitute genetic clusters in accordance with chromosome number or ecology. Additionally, to investigate their evolutionary relation to other Cochlearia species, Icelandic plants were compared to recognized diploid species in Svalbard (C. groenlandica) and southwestern Europe (C. pyrenaica and C. aestuaria). Analyses of SNP data showed that Icelandic plants cluster according to ecology, and not according to chromosome number. Furthermore, the genetic variation among the Icelandic populations display a geographic pattern, where plants sampled in closely located sites are more similar irrespective of chromosome number. Icelandic plants do not cluster with southwestern European plants, but alpine (2n = 14) plants on Iceland consistently group with C. groenlandica in Svalbard. Based on the results from this study, it is suggested to refer alpine Icelandic plants to C. groenlandica. The Icelandic coastal plants show no clear genetic or morphological separation between plants with different chromosome number (2n
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