Appendix and data files

Appendix 1 and 2 were used in the main text. Four original data files were used to conduct the analyses

Sequences alignments and morphological data

NEXUS and PHYLIP format .txt files for concatenated UCE alignments. NEXUS format .txt files for individual UCE alignments. CSV format .txt file with summary morphological data, NEWICK format tree files, and R script used in comparative analyses

Supplementary Figure S4

FIGURE S4. Estimates of gene trees for individual UCEs are poorly resolved. Box plot showing the number of resolved branches when those branches with <50% support in ML bootstrap analyses (using the indicated programs) or posterior probabilities <0.5 (using MrBayes). Similar data are shown for the optimal tree identified using GARLI with very short branches collapsed to form a polytomy (‘GARLI-opt’). Numbers of parsimony informative sites per UCE are used to define the sets of UCEs considered (‘all’ indicates that all UCEs with at least one parsimony informative site were included)

Meiklejohn et al. UCE alignments, unedited

gzipped tar file containing 1479 individual nexus files, each with a UCE alignmen

Meiklejohn combined evidence data file

gzipped nexus file with all data (after the editing described in the text). All of the individual UCEs, nuclear introns, and mitochondrial gene regions are indicated using CHARSETS. Partitioning schemes identified using PartitionFinder are also included

Regime Change Policy interventions: Iraq and Libya

This bachelor's thesis aims to prove or disprove following hypothesis: The interests of western countries have major impact on the present instable situation in the Middle East and North Africa region. First, theoretical chapter defines area of case studies, explains legality and legitimacy, and interprets the national security strategy of the US from 2002, which is also known as Bush doctrine or Regime Change doctrine. Empirical part consists of two case studies: intervention in Iraq 2003 and inervetion in Libya 2011. These case studies are focused on political, economic and cultural context of the interventions. The last part compares Iraq and Libya and both interventions, while searching for a trend that might have the destabilizing effect

Supplementary Figure S1

FIGURE S1. Example of a UCE alignment showing a short mismatch at one end. This portion of the alignment shows no variation with the exception of a stretch of 13 nucleotides with nine mismatches. Similar stretches are evident in 69 UCE alignments. The terminal gaps in three other taxa simply reflect the failure of those assemblies to extend all of the way to the end of the alignment

Supplementary Figure S3

FIGURE S3. Performance of the maximum parsimony (MP) criterion for phylogenetic estimation with UCE data. The topology of the single most parsimonious tree of 50929 steps recovered when UCE data were analyzed (A) was identical to the ML tree for those data. Minimum branch lengths for UCEs (i.e., the number of unambiguous synapomorphies) are shown above branches and bootstrap support is presented below branches. An MP analysis of combined UCEs+introns+mitochondrial data also yielded a single tree (of 59964 steps) with an identical topology. Bootstrap support for both analyses is reported as a percentage of 500 replicates. Full (100%) support is indicated using an asterisk (*). MP and ML branch lengths for the UCE data were strongly correlated (B), suggesting that the MP criterion is likely to have reconstructed character state transformations accurately. The graph was limited to internal branches

Supplementary Figure S2

FIGURE S2. Number of variable (left) and parsimony informative (right) sites present in each UCE locu

Reddy_sup_fileS2_PrumLoci

Information about the loci used by Prum et al. 2015. An xlsx file with two sheets ("README" and "Prum locus information")