Additional file 2: of Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex
Creators: name: Ericson, Per
name: Yanhua Qu
name: Rasmussen, Pamela
name: Mozes Blom
name: Rheindt, Frank
name: Irestedt, Martin
Publisher: name: figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Supplementary tables and figures. Table S1 Data sets used for reference mapping. Table S2 Comparison of different tree topologies reconstructed in the phylogenetic analyses of different data sets and by employing different methods. Note that several topologies are incompatible with each other. Table S3 Calculated effective population sizes (Ne) inferred by G-PhoCS using the predefined tree topology in Fig. 2 (after pruning palawanensis from the tree, see text in Additional file 1 for details) and after calibrating the estimated parameter θ assuming an average mutation rate of 4.6*10− 9substitutions per generation and an average generation length of 4.2 year. Table S4 Calculated divergence times (T) inferred by G-PhoCS using the predefined tree topology in Fig. 2 (after pruning palawanensis from the tree, see text in Additional file 1 for details) and after calibrating the estimated parameter τ assuming an average mutation rate of 4.6*10− 9 substitutions per generation and an average generation length of 4.2 year. Table S5 Estimates of mean number of migrants per generation (Ms-t) for the migration bands inferred by bands inferred by G-PhoCS using the predefined tree topology in Fig. 2 (after pruning palawanensis from the tree, see text in Additional file 1 for details). Table S6 Comparisons of estimates of divergence times for major clades within the “Pitta sordida species-complex” using a molecular clock approach in Beast2 and genomic mutation rates in G-PhoCS. In the G-PhoCS analysis we used two different estimates of the mutation rate in passerines; 3.0*10− 9(Zhang et al. 2014) and 4.6*10− 9(Smedset al. 2016). Table S7 Individuals and scaffolds in which longer (&gt; 250 Mb) stretches of homozygosity was observed. Table S8 The f4-statistic was calculated in four-taxon comparisons to test different hypotheses of introgression. Table S9 Analysis of mismatch distribution in populations within the “Pitta sordida species-complex” from which two or more individuals were sampled. Table S10 Admixture signatures from D-statistic (ABBA-BABA test). Table S11 Alternative taxonomic classifications of the taxa included in the “Pitta sordida species-complex”. Table S12 Specimen data for the samples used in the study. Table S13 Mapping coverage estimated with genomecovin BEDToolsv.2.26.0. Figure S1 Phylogenetic relationships within the “Pitta sordida” species-complex reconstructed with a neighbor-joining analysis of 2,193,399 high-quality SNPs. Figure S2 Phylogenetic relationships within the “Pitta sordida” species-complex inferred with MP-EST. Figure S3 Phylogenetic relationships within the “Pitta sordida” species-complex inferred with MP-EST. Figure S4 Posterior distribution of trees obtained in a Bayesian analysis using SNAPP based on 22,074 biallelicSNPs shared across the taxa in the western clade. Figure S5 Posterior distribution of trees obtained in a Bayesian analysis using SNAPP based on 17,810 biallelicSNPs shared across the taxa in the eastern clade. Figure S6 Principal component analysis (PCA) of the genomic variation among the samples assigned to the taxa mulleri, cucullataand bangkana. Figure S7 Divergence times and effective population sizes (Ne) inferred by G-PhoCSusing the predefined tree topology from Fig. 2 (after pruning palawanensis, see Additional file 1). Figure S8 D-statistic (ABBA-BABA) for the tested comparisons within the western clade. Figure S9 D-statistic (ABBA-BABA) for the tested comparisons within the eastern clade. Figure S10 Cumulative size of the genome fraction allocated in runs of homozygosity (&gt; 250 kb) per sample. Figure S11 Cumulative size of the genome fraction allocated in runs of homozygosity (&gt; 250 kb) plotted against the size of the island from where the sample was collected. Figure S12 Variation in effective size (Ne) in populations represented by more than one individual inferred with the approximate Bayesian computation pipeline PopSizeABC using 1,304,779 SNPs. Figure S13 Scatterplot of the genetic (p-distances) and geographic distances (km) between all pairs of samples in the western clade. Figure S14 Scatterplot of the genetic (p-distances) and geographic distances (km) between all pairs of samples in the eastern clade. (PDF 1643 kb)