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).