4 DISCUSSION
4.1 Genetic diversity in different parts of
Eurasia
In this study, we reported both nuclear and mitochondrial genetic
diversity of golden eagles for the entire Eurasia with newly sampled
regions, such as Russia and Central Asia. Our analyses of nuclear
microsatellites and mitochondrial sequences revealed a relatively high
level of genetic variation in the Eurasian golden eagle population,
being the highest in Central Asia and Caucasus, and the lowest in
Northern Europe.
Mitochondrial genetic diversity in Central Asia and Caucasus (h = 0.82,
π = 0.018) was similar to the former findings on golden eagles from
mainland Asia (h = 0.79–0.93, π = 0.009–0.012; Nebel et al. ,
2015, 2023). Among the previous studies, nuclear genetic diversity was
reported only for the Mongol-Altai region, where a slightly higher
observed heterozygosity (HO = 0.58) but lower expected
heterozygosity (HE = 0.59) and allelic richness (AR =
4.07) were found compared to Central Asia and Caucasus
(HO = 0.51, HE = 0.66, AR = 4.98).
Notably, our samples from this region dated from 1898 to 1950 (N = 14),
with four individuals of unknown year, while Nebel et al. (2023)
analyzed the contemporary population. Therefore, despite the small
sample size, the observed differences in nuclear genetic diversity may
suggest either temporal changes or small-scale genetic variations within
mainland Asia. The high genetic diversity in Central Asia detected in
our study and in the previous studies, aligns with expectations for
areas near past glacial refugia (Hewitt, 2000), the central-marginal
hypothesis (CMH, Eckert et al. , 2008), and the latitudinal
genetic diversity gradient hypothesis (Smith et al. , 2017;
Fonseca et al. , 2023).
On the other hand, mitochondrial diversity was the lowest and nuclear
diversity also low in Northern Europe. While peripheral populations
commonly have lower genetic diversity compared to populations at the
core of the distribution (Eckert et al. , 2008), the observed
heterozygosity in Northern Europe (HO = 0.50) was even
lower than in previously studied north European continental populations,
including Finnish (HO = 0.57; Kylmänen et al. ,
2023), Norwegian (HO = 0.56; Nebel et al. , 2023),
and Finnish-Estonian (HO = 0.62; Nebel et al. ,
2023) populations, with the exception of Scotland (HO =
0.46; Ogden et al. , 2015). Since most of our samples from
Northern Europe were from the Northwestern federal district in Russia,
our results imply that this area has especially low genetic diversity
compared to other northern European regions.
Central and Eastern Europe exhibited similar levels of observed
heterozygosity but higher expected heterozygosity (HO =
0.47, HE = 0.61) compared to previously studied golden
eagles in the Slovakian population (HO = 0.44,
HE = 0.49; Bielikova et al. , 2010) and in the
Alps and Mediterranean region (HO = 0.51,
HE = 0.55; Nebel et al. , 2023). Additionally, we
noted higher mitochondrial genetic diversity in this group compared to
the Alpine and Mediterranean region (h = 0.69, π = 0.008; Nebel et
al. , 2023), regardless of whether the analyses included only our
samples (h = 0.75, π = 0.014) or also GenBank sequences (h = 0.76, π =
0.016). Central and Eastern Europe group contained samples mainly
originating from European Russia; thus, the observed high genetic
diversity may point to that European Russia harbors a significant
reservoir of genetic diversity among European golden eagles.
4.2 Mediterranean and Holarctic groups: genetic diversity
and demographic
history
By including samples from previously unexplored regions of the golden
eagle distribution, we were able to better visualize the spatial
distribution of the two mitochondrial lineages and compare it with the
findings from nuclear markers. The Holarctic lineage was more
widespread, with nearly twice as many golden eagles carrying these
haplotypes (N = 284) compared to the Mediterranean lineage (N = 150).
Previous studies of large raptors found that range size and historical
population size were strong determinants of current genetic diversity
(Väli et al. , 2019). Here we discovered that the Holarctic group,
occupying a larger geographical range, also had higher mitochondrial
genetic diversity than the Mediterranean group. However, the latter
exhibited higher allelic and private allelic richness, while other
estimates of nuclear genetic diversity were comparable. The
Mediterranean group also showed consistent signs of demographic
expansion, which could have contributed to an increase in nuclear
genetic diversity, whilst almost all demographic analyses pointed to a
stable population size of the Holarctic group. The inclusion of samples
from previously unstudied areas and temporal periods resulted in slight
shifts of the estimated mitochondrial genetic diversity compared to the
earlier reports by Nebel et al. (2015); we observed a slight
reduction in haplotype and nucleotide diversities in the Holarctic group
(h = 0.61 and 0.75, π = 0.0039 and 0.0041, in this study and in Nebelet al. (2015), respectively), and a slight increase in these
parameters in the Mediterranean group (h = 0.60 and 0.58, π = 0.0028 and
0.0020).
Our finding of Mediterranean haplotypes in both Central and Eastern
Europe and Central Asia and Caucasus suggests that the Mediterranean
lineage is spread more eastwards than thought before, where it now
coexists with the Holarctic lineage, resulting in high genetic diversity
in this region. The Mediterranean lineage likely survived in a glacial
refugium around the Mediterranean region, as previously suggested by
Nebel et al. (2015), but the location of a refugium for the
Holarctic lineage remains uncertain; perhaps it was somewhere in
central-eastern Asia. The Mongolian Plateau and the Altai-Saiyan
Mountains have been suggested as glacial refugia for several plant and
mammal species (e.g., Hais et al. , 2015; Lv et al. , 2016;
McLean et al. , 2018), making them plausible candidates also for
the golden eagle, especially in the light of the recently discovered
golden eagle’s genetic diversity hotspot in the Mongol-Altai region
(Nebel et al. , 2023).
4.3 The north-south genetic gradient in Eurasian golden
eagles
We discovered both a north-south genetic gradient and genetic
differentiation among the geographical groups in Eurasian golden eagles
with both mitochondrial and microsatellite analyses. While the two
mitochondrial lineages were identified and comprehensively discussed by
Nebel et al. (2015), no evidence of their division was associated
with nuclear markers. In addition, we highlighted the genetic uniqueness
of the Central Asia and Caucasus and the Northern Europe groups in
Eurasian golden eagles.
The latitudinal genetic gradient can originate due to several factors,
including climatic and environmental instability in the north (Eckertet al. , 2008; Smith et al. , 2017), differences in
migratory flyways (Monti et al. , 2018), postglacial colonization
history (Thörn et al. , 2021), and a combined influence of the
Quaternary climatic changes (Fonseca et al. , 2023). For example,
a large-scale study of ospreys (Pandion haliaeetus ), identified
two genetic clusters in Eurasia: Mediterranean and Eurasian, which were
attributed to different migratory flyways (Monti et al. , 2018).
Interestingly, the genetic clustering of ospreys was geographically
similar to the genetic clustering observed in Eurasian golden eagles.
However, the migratory flyway theory is not applicable to golden eagles
because Eurasian golden eagles are generally non-migratory (Watson,
2010). On the other hand, the genetic differentiation between the north
and the south as a result of post-glacial colonization history is
supported by our findings of genetic diversity and demographic history
(see above). Furthermore, golden eagles occupy a variety of habitats,
implying diverse dietary and nesting adaptations. Their distribution in
southern Eurasia covers Mediterranean-rich habitats, mountains, and
steppes, while in northern Eurasia, they are predominantly found in
mixed forests and taiga (Watson, 2010). This distinct ecological
variation may be a potential underlying reason for the observed genetic
differentiation.
However, although this gradient resulting from mixing of two divergent
lineages seems to exist, we did not find evidence for isolation by
distance (IBD) among the Eurasian golden eagles. Lack of an IBD pattern
may be explained by the high dispersal capacity of golden eagles,
especially of adolescent birds, documented in multiple studies (e.g.,
Nygård et al. , 2016; Poessel et al. , 2022). High dispersal
potential leading to high gene flow was also mentioned as a reason for a
lack of the IBD pattern in British golden eagles (Bourke et al. ,
2010) and in some large-scale studies of other philopatric raptors, such
as the Eurasian kestrel (Falco tinnunculus ; Alcaide et
al. , 2009) and the greater spotted eagle (Clanga clanga ; Väliet al. , 2019).
4.4 Temporal genetic variation and demographic
history
The population bottleneck of the
19th–20th centuries has left
genetic signs in Palearctic golden eagles. First, we noticed a decrease
in the number of haplotypes. While it is possible that the absence of 14
haplotypes in the post-bottleneck period compared to the bottleneck
period was due to incomplete sampling, the rarefaction-extrapolation
analyses indicated that the Bottleneck group had a significantly higher
number of haplotypes compared to the Post-bottleneck group. Second, we
observed a decrease in allelic and private allelic richness; a signal of
a population bottleneck, as rare alleles are lost at a faster rate than
heterozygosity is decreased (Allendorf, 1986). Third, the Bayesian
Skyline Plot (BSP) analyses showed a reduction in the effective female
population size (Nef) in the Eurasian population
starting around 1975, aligning with known population declines in many
populations across Eurasia (e.g., Bielikova et al. , 2010; Nebelet al. , 2015; Ollila, 2019; Starikov, 2020). Finally, when
comparing temporal variation between the Mediterranean and Holarctic
lineages, we found that in both lineages, genetic diversity was higher
prior to the recent population bottleneck.
Despite the population bottleneck, golden eagles have nevertheless
retained relatively high levels of genetic diversity. Factors such as
long generation time, admixed origin of populations, and large
distribution range contribute to high genetic diversity (Avise, 2000;
Hailer et al. , 2006; Väli et al. , 2019). Therefore, as
golden eagles are long-lived (Watson, 2010), occupy vast geographical
areas (BirdLife International & Handbook of the Birds of the World,
2022), and likely originate from several glacial refugia (Nebel et
al. , 2015; see above), these factors have undoubtedly played an
important role in maintaining their genetic diversity. Similarly, high
genetic diversity has been observed in other Eurasian raptors, such as
the white-tailed eagle (Hailer et al. , 2007), the cinerous
vulture (Aegypius monachus , Poulakakis et al. 2008), the
crowned solitary eagle (Buteogallus coronatus ; Canal et
al. , 2017), and the greater spotted eagle (Väli et al. , 2019).
While the long generation time may have buffered the effects of the
19th–20th-century bottleneck, it is
also possible that the recent population decline was not severe enough
to cause significant reductions in golden eagle’s genetic diversity
(Bourke et al. , 2010). Noteworthy, the bottleneck of the
19th–20th centuries might have
occurred at various time points in different parts of Eurasia,
distorting the detection of temporal genetic diversity changes on a
large-scale. Unfortunately, no studies on long term population trends in
golden eagles have been conducted in Russia or elsewhere in continental
Asia. For example, the only available records in central Yakutia state
that the species was commonly nesting until the mid-1950s but became
rare and disappeared from some areas in 1970–1980s, and only during the
last 15–20 years the population has started to grow (Isaev et
al. , 2021). Similarly, no golden eagle nests were found in Dauriya
(east of the Lake Baikal, Zabaikalskiy krai) for the period from 1950s
until 1990s (Karyakin & Nikolenko, 2012). On the other hand, nesting in
the upper parts of the Don River basin (European Russia) was questioned
already in the beginning of the 20th century, but the
encounters became more frequent since the mid-1960s (Semago, 2006).
Similarly, in Kazakh uplands (Kazakhstan), golden eagles were only
reported since 1960s (Starikov, 2020).
When interpreting the population history of golden eagles, it is, too,
essential to consider the significant impact of major glaciations on the
distribution and dynamics of species (Hewitt, 2004). The glacial periods
have had a huge impact on species’ ranges through dispersal,
contractions, and even extinctions (Hewitt, 2000). In our study, we
detected signals of population expansion of golden eagles in Northern
Europe, a region that was long covered by the Scandinavian Ice Sheet.
During the last glacial period, the Scandinavian Ice Sheet was the
largest component of the Eurasian ice sheet complex, and it covered
Fennoscandia and North-Western Russia repeatedly (Hughes et al. ,
2016). Upon the end of the Last Glacial Maximum (26.5–19 ka; Clarket al. , 2009), species began to re-colonize new regions as the
ice retreated (e.g., Ersmark et al. , 2019; Behzadi et al. ,
2022). Although the precise routes of recolonization of Northern Europe
remain uncertain, one possible direction could have been from the east
of Eurasia, due to the prevalence of Holarctic haplotypes over the
Mediterranean ones in this region.