1 INTRODUCTION

Throughout history, humans have had a considerable impact on the distribution and viability of wild animal populations. This influence has become increasingly prominent during the last centuries due to, for example, overexploitation and habitat destruction (Newton, 2003; Dirzoet al. , 2014). As a result, many populations have become small, fragmented, or even extinct (Young et al. , 2016). The drastic declines in population sizes are known as population bottlenecks. Population bottlenecks have profound consequences for the genetic viability, adaptability, and long-term viability of species (Frankhamet al. , 2010). Small population size leads to genetic drift, loss of genetic variation, increased risks of inbreeding depression, and overall higher genetic load (Amos & Balmford, 2001; Díez-del-Molinoet al. , 2018). The extent of these consequences depends on the severity of the population bottleneck: how fast the decline happens (in generations) and how many individuals are left (Amos & Balmford, 2001). Therefore, while some species are confronted with alarming rates of inbreeding and loss of genetic variation as a result of a sharp population contraction (e.g., Ewing et al. , 2008), others have been thriving for hundreds and thousands of years despite small population sizes and low genetic diversity (e.g., Milot et al. , 2007; Johnson et al. , 2009).
Multiple factors may affect the viability of species and the outcomes of population bottlenecks. For instance, a long generation time has been argued to have a profound influence on buffering the deleterious effects of bottlenecks and long-persistent small populations by reducing the impact of genetic drift (Amos & Balmford, 2001). Furthermore, populations on the edge of the species’ distribution commonly exhibit lower genetic diversity compared to populations near the core of the distribution due to smaller effective population sizes (Ne), reduced gene flow, and stronger geographical isolation (Vucetich & Waite, 2003; Eckert et al. , 2008). Lower genetic diversity and greater differentiation of peripheral populations are the main features of the central-marginal hypothesis (CMH), which has been confirmed in many studies (e.g., Schwartz et al. , 2003; Eckert et al. , 2008; Langin et al. , 2017; Rönkä et al. , 2019), but also contradictory evidence exits (e.g., Sagarin & Gaines, 2002; De Kort et al. , 2021). Another important geographical aspect that influences genetic diversity is proximity to the past glacial refugia. Glacial refugia served as havens for species that were affected by climate cooling by providing favorable habitats which allowed populations to survive and maintain genetic variation. As a result of postglacial expansion, populations in close proximity to the refugia typically show higher levels of genetic diversity, whereas populations on the expansion frontier have lower genetic diversity (Hewitt, 2000). Finally, for many species, greater intraspecific genetic variation has been found in southern regions compared to northern ones, because of a more stable environment and larger population sizes in the lower latitudes (Smith et al. , 2017; Fonseca et al. , 2023).
The golden eagle (Aquila chrysaetos ) is a long-lived raptor with a wide Holarctic distribution (BirdLife International, 2023). As a predator of game animals and domestic livestock, the species has been heavily persecuted across Europe and North America (e.g., Watson, 2010). In addition to direct persecution, golden eagles have suffered from urban growth and forestry due to their sensitivity to anthropogenic disturbances (Watson, 2010). Altogether, these have resulted in local extinctions of golden eagles in various parts of their range (e.g., Ireland, southern Finland, and lowlands of central Europe), and in overall population declines across the Holarctic region during the 19th–20th centuries (e.g., Bielikova et al. , 2010; Nebel et al. , 2015; Ollila, 2019; Starikov, 2020). Golden eagles were protected in most parts of their distribution by the end of the 20th century (e.g., Below, 2000; Whitfield et al. , 2008; Sato et al. , 2017). As a consequence of conservation efforts and the species’ extensive range, the golden eagle is currently classified as Least Concernby the International Union for Conservation of Nature (IUCN) both globally, and in Europe (BirdLife International, 2023). The classification reflects the overall stability, but regional populations continue to face local threats, such as habitat destruction, human disturbances, use of lead bullets and pesticides, collisions with wind turbines, and illegal trade (e.g., Watson, 2010; D’Addario et al. , 2019; Slabe et al. , 2022). Unfortunately, some vast regions within the species’ distribution, such as Russia and much of Asia, are lacking data on golden eagles, limiting conservation efforts. For example, only a few small-scale scientific expeditions have been organized to collect information on breeding, ecology, and distribution of golden eagles in Russia, Kazakhstan, and Mongolia (e.g., Shagdarsuren, 1964; Smelansky et al. , 2020; Isaev et al. , 2021). These expeditions have revealed that the species is generally rare in many parts of Russia and Kazakhstan, and that there has been a noticeable decline in their numbers in several regions in recent times (e.g., Kerdanov & Nikolaev, 2019; Kazansky & Babushkin, 2021).
Nevertheless, the first studies that used population genetic tools for golden eagles revealed interesting insights of their population history (e.g., Bourke et al. , 2010; Judkins & van den Bussche, 2017; Naito-Liederbach et al. , 2021; Nebel et al. , 2019, 2023). For example, using global golden eagle data, Nebel et al. (2015) identified two distinct mitochondrial lineages: a Mediterranean and a Holarctic. Holarctic haplotypes were found across Europe, Asia and North America, while the Mediterranean lineage was restricted to the Mediterranean region (Nebel et al. , 2015; Judkins & van den Bussche, 2017). A subsequent study using microsatellites demonstrated genetic differentiation between Northern (Norway, Finland and Estonia) and Southern (Mediterranean and Alpine regions) Europe, with a distinct population in Scotland (Nebel et al. , 2019). However, the detected nuclear differentiation was not identical to the differentiation of the mitochondrial lineages (Nebel et al. , 2019). Meanwhile, genetic research on golden eagles in Asia remains sparse, with the exception of the extensive works on Japanese golden eagles (Masuda et al. , 1998; Sato et al. , 2017; Naito-Liederbach et al. , 2021) and a recent study in the Mongol-Altai region (Nebel et al. , 2015, 2023).
Here we aimed to improve the knowledge on phylogeography of Eurasian golden eagles by incorporating previously undersampled regions, such as Russia and Central Asia. Using a combination of mitochondrial and nuclear genetic markers, we re-evaluated population structure and genetic differences between golden eagle populations in the Palearctic. In addition, we studied demographic history and the effects of the recent population bottleneck on the genetic variation of this species.