Figure legends
Figure 1. Distribution of T. ruficapillus , sampling information and analyses of mitochondrial DNA. (a) Distribution map (shaded in violet) showing sampling localities, subspecies identity and the type of sequence data obtained for each sample. The distribution map is based on BirdLife International and NatureServe (2014). (b) Median-joining haplotype network of concatenated mDNA (COI + cyt b ; 1,130 bp). Circles represent haplotypes and their size is proportional to haplotype frequency. The length of the branches connecting haplotypes is proportional to the number of nucleotide differences between them, which are indicated by the number of line marks on each branch. Colors represent the subspecies according to the scheme incorporated in the figure. Black circles represent unsampled hypothetical haplotypes. Bird illustrations are from del Hoyo (2020). (c) Bayesian phylogenetic tree with divergence times obtained from the analysis of the concatenated mitochondrial dataset (1,130 bp). The numbers near the nodes indicate the mean divergence time estimates and the numbers between square brackets correspond to the 95% highest posterior density intervals of those estimates. Divergence times and the numbers between square brackets are in millions of years ago. Posterior probability values are shown below the divergence times. The colors to the right of the tree indicate subspecies information.
Figure 2. Genomic analyses of T. ruficapillus . (a) Principal Component Analysis (PCA) based on 2,306 SNPs (SNPs present in all individuals). (b) Structure plot for K=3 based on 5,073 SNPs (one random SNP per RAD locus). (c) Phylogeny inferred with maximum likelihood; the colours to the right of each individual indicate the subspecies. The tree was rooted with Thamnophilus caerulescens . Bootstrap support values are indicated in the nodes.
Figure 3. Demographic reconstruction of T. ruficapillus based on 6,165 RADseq loci (13,485 SNPs). Estimates of divergence times (T; in millions of generations), migration rates (mg; in migrants per generation) and current and ancestral effective population sizes (Ne; in millions of individuals) are reported with their 95% confidence intervals.
Figure 4. Analysis of the vocalizations of T. ruficapillus . Song differentiation among subspecies is shown based on a PCA performed with the song variables (mean duration of the note, mean duration of the interval between notes, fundamental frequency, bandwidth of the note and the number of notes in each song; the first four variables were measured for the first note).