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 (A –C , N = 91) and mitochondrial
lineage groups (D –F , 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.