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Phylogenetic Relationships of Silene Sect. Melandrium and Allied Taxa

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Phylogenetic Relationships of Silene Sect. Melandrium and Allied Taxa ! "#! $ %&'(%)($ *++%,-,./,0 *+)%12.,.--0.1-,,. ! 3 4 3 3!!35.,6626 !" # $%&%&&'&'()&* * * + ,- . , / ",%&&',+ / *, " - 0 1 * $ 2 -," , 3)',4& , ,'5!6' 6774657 63, -* *8 0 1 " 9 * : * , * 8 ," . ; * : * , * * 0 1,- * * ,- " ,- ; : * . , < . ** * =>? . 6 +/ ,- ; , " * , ! , $ 8* " ,@ * * ,* ! * , - . * **, "# $= $ = =-"=- " "/" /+"%/+%/+%=> =? <-= @ %&' ( ) *+,-./# A" 8/ %&&' <== 37 63% 4 <='5!6' 6774657 63 ( ((( 6 &&!&30 (BB ,:,B C D ( ((( 6 &&!&31 Cover illustrations: Barry Breckling, Sara Gold, Kjell Lännerholm, Anja Rautenberg and Wiebke Rautenberg. List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Rautenberg, A., Filatov, D., Svennblad, B., Heidari, N., Oxel- man, B. (2008) Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene. BMC Evolutionary Biology, 8:299 II Rautenberg, A., Hathaway, L., Oxelman, B., Prentice, H. C. Phylogenetic relationships of Silene section Elisanthe (Caryo- phyllaceae) as inferred from chloroplast and nuclear DNA se- quences. Manuscript. III Rautenberg, A., Hathaway, L., Prentice, H. C., Oxelman, B. Phylogenetic relationships and optimal genealogical species de- limitations of Silene section Melandrium (Caryophyllaceae). Manuscript. IV Sloan, D. B., Oxelman, B., Rautenberg, A., Taylor, D. R. Phy- logenetic analysis of mitochondrial mutation rate variation in the angiosperm tribe Sileneae. Submitted. V Rautenberg, A., Sloan, D. B., Aldén, V., Oxelman B. Phyloge- netic relationships of Silene multinervia and Silene section Conoimorpha (Caryophyllaceae). Manuscript. AR was responsible for the writing of all papers, except IV, with help of the co-authors. AR was responsible for most of the lab work in I and III, parts of the lab work in II and V, and all analyses in papers I–III and V. The defen- dant’s contribution to paper IV is restricted to providing DNA material and comments to the analyses and the text. Contents Introduction.....................................................................................................9 Gene trees and species trees .......................................................................9 On the existence of species..................................................................11 Study species............................................................................................11 Aims .........................................................................................................14 Materials and Methods..................................................................................15 Paper I (Conflicting phylogenetic signals in the SlX1/Y1/SlXY1 genes).......17 Paper II and III (Relationships of Silene section Melandrium).....................20 Paper IV (Mitochondrial mutation rate variation) ........................................25 Paper V (Relationships of S. multinervia and S. section Conoimorpha) ......27 Conclusions...................................................................................................31 Summary in Swedish (Sammanfattning på svenska)....................................32 Fylogenetiskt släktskap bland Silene sektion Melandrium och närbesläktade grupper ..............................................................................32 Acknowledgements – Tack – Danke – W ..........................................35 References.....................................................................................................38 Abbreviations bp base pairs cpDNA chloroplast DNA BEAST Bayesian Evolutionary Analysis Sampling Trees BEST Bayesian Estimation of Species Trees HPD highest posterior density MRCA most recent common ancestor mtDNA mitochondrial DNA mya/kya million/thousand years ago RS absolute synonymous substitution rates Introduction “A man with one clock always knows the time. A man with two clocks is never sure” could for this study be translated to something like “A phyloge- neticist with one tree always (thinks she) knows the true relationships. A phylogeneticist with two trees is never sure”. Systematic biology deals with evolutionary relationships among organisms, often depicted by phylogenetic trees. These trees are nowadays usually based on the DNA sequences of different organisms and use mathematical models to infer a plausible graph over the organisms’ relationships. A challenge in phylogenetic research is that the relationships between or- ganism lineages are not always straightforward processes that are reflected in every part of the organisms’ genomes. The observation that phylogenies sometimes tell us conflicting stories is, however, also one of the advantages with using molecular data: by investigating the unexpected patterns we find, we can learn more about the evolutionary processes that act on us and the world around us. Gene trees and species trees Different genes within an organism can have different evolutionary histories, because of e.g. mode of inheritance, events of sexual reproduction (hybridi- zation), or incomplete lineage sorting. In most flowering plants, chloroplasts and mitochondria are maternally inherited (through the egg cells). As a re- sult, the genetic material present in chloroplasts and mitochondria will re- flect the evolutionary history of the maternal lineage only. The nuclear ge- nome, on the other hand, will be inherited from both parents, and thus both parental lineages will be reflected in the nuclear genome. Chloroplasts and mitochondria are therefore generally expected to depict the seed dispersal, whereas nuclear DNA is expected to depict both seed and pollen dispersal patterns. A successful hybridization event leads to mixing of genes from two independent lineages into the progeny. When a lineage splits into two, ances- tral alleles might be randomly sorted in the new lineages (incomplete lineage sorting), which also will result in conflicting gene trees. When different gene trees give different topologies, one would often like to find a tree that summarizes the species’ history (Figure 1). There are dif- ferent ways to infer species trees from gene trees. One way is to concatenate 9 the data from different genes and use all information to produce a single tree. This method is appropriate if all the included genes have the same history, but if they have not, the result might be misleading (Kubatko and Degnan 2007). An alternative is to compare the separate gene trees and select the topology that occurs most frequently as the species tree. A problem with this approach is that the gene tree topology that is most likely to evolve from the species tree can differ from the species tree topology (Degnan and Rosenberg 2006). A third approach is to take into account the possibility of random differential survival of ancestral alleles in the daughter lineages in a coalescent framework (Maddison 1997; Maddison and Knowles 2006; Ed- wards et al. 2007). In coalescent theory, gene copies in a current population are traced back to their most recent common ancestor, while taking into ac- count population size and population structure. AB C A } B } } } time Figure 1. One way to view species is to imagine them as “tubes”, in which the evo- lution operates on the genes in individuals and populations. Here are three different gene phylogenies included in a “species” tree, where the outer thick, black lines represent organism lineages (taxa). The thin, black lines represent genes that are reciprocally monophyletic within taxa. The light grey lines represent gene copies that are more similar across the taxa A and B than within the taxa, because of in- complete lineage sorting (deep coalescence). The thin, dark grey lines represent a gene split that has occurred after the divergence of A and B, best explained by hy- bridization. 10 On the existence of species When referring to “species trees” we assume that there is such a thing as species. In reality, when working with closely related species, it is not al- ways easy to draw the limits between species. There is no clear-cut distinc- tion between various taxonomic levels like varieties, races, subspecies, and species. With an open mind on species definitions, it can be interesting to explore what impact different a priori taxon delimitations have on the interpretations of conflicting gene trees. Imagine a case when the sampled gene trees are incongruent and all genes are not reciprocally monophyletic within taxa (Figure 1). It can here be reasonable to explore whether the sampled gene trees favour separate A and B lineages, or whether the genetic subdivision between A and B is so low that they can be considered one species. By choosing classifications that maximize the likelihood of the observed gene trees, we have a way to optimize species delimitations. Study species The plant genus Silene L. (Caryophyllaceae) consists of around 650 mostly herbaceous species, with a centre of diversity in the Mediterranean and Southwest Asia. Silene and the closely related smaller genera Agrostemma, Atocion, Eudianthe, Heliosperma, Lychnis, Petrocoptis, and Viscaria are often referred to as Sileneae (Oxelman et al. 2001). The studies presented
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