Species Delimitation and Phylogenetic Relationships. A study of Silene sections Atocion and Cryptoneurae

Abstract: Abstract The existence of conflicting genealogies of different genes through the evolution of species complicates the inference of phylogenetic relationships. The Multispecies Coalescent (MSC) model provides a theoretical background that account for the stochasticity in the genealogical process, thus providing systematists with a potentially objective way of testing alternative hypotheses of putative species. This thesis focus on species delimitation under the MSC model with particular reference to Silene L. (Caryophyllaceae) sect. Cyptoneurae Aydin & Oxelman and sect. Atocion Otth. A phylogenetic overview of both sections including several taxonomic conclusions are presented. Based on extensive sampling of nuclear ITS and chloroplast rps16 markers across the tribe Sileneae, sect. Atocion and sect. Cyptoneurae are shown to be distantly related, despite strong morphological similarities. Section Cyptoneurae is formally described and a key to the included species is provided. Species limits within sect. Cryptoneurae are evaluated with the Bayesian methods BP&P and marginal likelihood estimation (MLE) with 'BEAST using data from six putatively independent loci. MLE score comparison is found to be an efficient way to evaluate alternative hypotheses of species delimitations. The recognition of a new species, S. ertekinii Aydin & Oxelman is strongly supported by both approaches. Species limits in sect. Atocion are investigated with the DISSECT method without conditioning on any classification defined a priori. MLE scores of morphological classifications estimated with 'BEAST are found to be inferior to classifications recognising strongly supported minimal clades from the DISSECT results, which reveal strong support for the recognition of several new species in the section. Two lineages which belong morphologically to S. assyriaca Hausskn. & Bornmüller ex Lazkov are found to be distantly related, thus being cryptic species, as no morphological and geographical differentiation can be detected. Two major, geographically structured clades are found in the section. One of the two western lineages should be named S. atocioides Boiss., whereas S. aegyptiaca (L) L.fil. belong to the eastern clade. Silene delicatula subsp. pisidica Boiss. is shown to be synonymous to S. atocioides. Silene fraudatrix Meikle, considered by current taxonomy as an endemic species on Northern Cyprus, is not clearly distinct from some mainland populations of S. aegyptiaca and those on Cyprus. From one of the studied loci, an ancient recombination event resulting from a hybridization event between the eastern and western clades is detected. This study is one of the first that applies the MSC model for species delimitation in plants. The strengths and weaknesses of the approach are discussed, as well as the possible consequences to taxonomy and, in the long run, biodiversity estimation.