FIGURE LEGENDS

Figure 1. Median-joining haplotype network of a fragment of the mtDNA CR (326 bp) from golden eagles across the Northern Hemisphere using 82 sequences from this study and 581 sequences from previous studies . The 56 haplotypes are divided into the Mediterranean and the Holarctic mitochondrial lineages. Newly found haplotypes are indicated with red font, and the names correspond to a country where the haplotype was sampled: KAZ – Kazakhstan, UZB – Uzbekistan, IRN – Iran, KYR – Kyrgyzstan, and RUS – Russia. Other haplotypes are named according to the study that has first reported the haplotype. The size of the circle corresponds to the number of individuals with a particular haplotype. Nodes indicate one mutation step.
Figure 2. The locations of golden eagles with the Mediterranean and the Holarctic haplotypes from this (dark green and dark blue) and previous studies (light green and light blue; Nebel et al. , and Kylmänen et al. , 2023). The size of a circle corresponds to the number of golden eagles in the area or country with either a Holarctic or a Mediterranean lineage haplotype. Eurasian distribution range of golden eagles is shaded with dark grey color (BirdLife International & Handbook of the Birds of the World, 2022). The map was created in QGIS 3.10 (QGIS Development Team, 2022).
Figure 3. Population structure of golden eagles across Eurasia using 12 microsatellite loci. The results depict analyses of geographical groups (AC , N = 91) and mitochondrial lineage groups (DF , N = 87). A – STRUCTURE results of cluster assignment of golden eagles for K = 2 using the four geographical groups as LOCPRIOR. B – DAPC plot of the first two discriminant functions showing genetic differentiation of golden eagles from the four pre-defined geographical groups. DAPC is based on the first ten PCs that explain 54.8% of variation. C – PCA plot of golden eagles from the pre-defined geographical groups.D – STRUCTURE results of cluster assignment of golden eagles for K = 2 using a mitochondrial lineage as LOCPRIOR. E – DAPC results of nuclear genetic differentiation of golden eagles with the Mediterranean and the Holarctic mitochondrial lineages. DAPC shows the first discriminant function and is based on the first 40 PCs that explain 96.4% of variation. F – GenePlot of pairwise comparison of golden eagles with the Mediterranean and the Holarctic lineage haplotypes. The 5% and the 99% quantiles outline the range where genetic assignment of individuals into these groups is the most likely.
Figure 4. Comparison of Bottleneck (1817–1984) and Post-bottleneck (1985–2017) temporal groups of 393 Eurasian golden eagles from a 326 bp mtDNA CR alignment. A – Results of rarefaction-extrapolation analyses (iNEXT) for the number of haplotypes. Circle and triangle indicate the observed number of haplotypes in both groups. B – Temporal haplotype network, with haplotypes divided into Holarctic and Mediterranean mitochondrial lineages. The numbers in circles correspond to haplotype frequency. Haplotypes that are not found in the other group appear as small white circles. Solid lines connect extant haplotypes, and dotted lines connect the unsampled haplotypes. Nodes indicate the number of mutational steps between the haplotypes. Vertical lines connect haplotypes found in both groups.
Figure 5. Bayesian skyline plots of effective female population sizes (Nef) of Eurasian golden eagles over time for the total Eurasian population (top left) zooming in to 1800–2000s (top right), and for the two mitochondrial lineages separately. Changes in Nef (y-axis, logarithmic scale) across time (x-axis, calendar years) are presented as medians with 95% upper and lower confidence intervals. Note different scales of the axes.