We use novel implementations models including migration and incomplete lineage sorting to reconstruct phylogenetic histories and delimit species, primarily in the plant group Sileneae, but also in other taxa. The information comes from targeted loci from HybSeq protocols, whole genome sequencing, and transcriptomics. Standard bioinformatics pipelines are used for trimming, assembly, mapping, phasing, and multiple alignment of sequences, but we are also exploring novel approaches, especially with regards to phasing. Most computational efforts are devoted to Markov Chain Monte Carlo implementations, where we are exploring computational efficiencies in relation to data size.