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Here is a complete, academically rigorous English translation of the **Introduction** and **Chapter 1** from your dissertation. Scientific terminology, taxonomic names, and citation formats have been preserved according to international standards. Due to the length, the text is structured with clear headings for readability. If you need subsequent chapters translated or formatted for a specific journal/platform, just let me know.

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# INTRODUCTION

## Relevance and Current State of the Problem
Identifying and analyzing the mechanisms of speciation is one of the fundamental problems in evolutionary biology. In turn, assessing intraspecific diversity is crucial for understanding the evolutionary history of species and the processes underlying their divergence. This approach is particularly relevant when studying evolutionarily young (recently diverged) species (Ronce, 2014). Such studies gain additional significance when they are based on the analysis of phenotypic and genetic diversity in populations or species that are threatened with extinction (Shaffer, 2014). Currently, data on intraspecific diversity also play a key role within the interdisciplinary field of eco-evo-devo (ecological and evolutionary developmental biology), which examines how environmental factors influence ontogeny and how changes in organismal development drive evolution (Sandberg et al., 2025).

When studying speciation mechanisms in a specific animal group, we inevitably must address the following questions (Harrison, 2014):
1. What barriers to gene flow exist between populations or species, and to what extent do they restrict it?
2. When and why did these barriers arise, and is it possible to identify a primary one?
3. What is the geographic context of the identified barriers?
4. What role do natural and sexual selection, as well as genetic drift, play in the observed divergence?
5. Has the genomic architecture—the number, effect size, and genomic distribution of genes responsible for observed traits—changed as a result of established reproductive isolation?

Furthermore, it should be noted that observed divergence may sometimes "reverse," and adaptations vary in their impact on speciation. This raises an additional question: why do some adaptive processes lead to the cessation of gene flow, while others merely increase intraspecific diversity (Lowry, Hopkins, 2014)?

It is also important to emphasize that speciation is not always a prolonged process; sometimes it spans only a dozen or a hundred generations. This allows us to observe populations or species within a human lifetime and witness speciation in action (Boughman, 2014). In the context of young species, this highlights the significant role of anthropogenic factors.

Considering the above, we consider the recently diverged species of the *Hierofalco* group (Fuchs et al., 2015)—the lanner falcon *Falco biarmicus* (Temminck, 1825), laggar falcon *Falco jugger* (Gray, 1834), black falcon *Falco subniger* (Gray, 1843), saker falcon *Falco cherrug* (Gray, 1834), and gyrfalcon *Falco rusticolus* (Linnaeus, 1758)—to be exceptionally suitable models for studying the causes and extent of their divergence, as well as their current phylogenetic relationships. The study of this supra-specific group of diurnal raptors (genus *Falco*, family Falconidae, order Falconiformes) is complicated by their high mobility and the absence of postzygotic isolation—they can interbreed and produce fertile offspring (Eastham, Nicholls, 2005). Nevertheless, despite significant morphological similarities and overlapping ranges, these species retain differences accumulated during divergence (see Section 1.3). Both global and local populations of these large falcons are threatened and legally protected (see Section 1.2), primarily (Nikolenko, Karyakin, 2020) due to their long-standing role in human culture as hunting birds in falconry (Wilcox et al., 2019). The removal of birds from wild populations causes additional harm through the selective extraction of individuals with specific phenotypes, the most famous being the "Altai" morph, characterized by uniformly or partially dark plumage and commonly referred to as the "Altai falcon" (Karyakin, 2011).

Moreover, despite a rich history of taxonomic hypotheses for the *Hierofalco* group, primarily based on morphological data (Menzbier, 1882, 1895, 1916; Kleinschmidt, 1901; Sushkin, 1915; Kots, 1948; Dementyev, 1951a, 1951b; Vaurie, 1961; Stresemann, Amadon, 1979; Stepanyan, 1990; Pfeffer, 2009; Karyakin, 2011; Koblik, Arkhipov, 2014), the genetic variability and phylogenetic relationships among individual populations and species remain poorly understood. This is particularly true for the saker falcon *Falco cherrug* (Gray, 1834) and gyrfalcon *Falco rusticolus* (Linnaeus, 1758) inhabiting Russia, as their "domestic" populations are underrepresented in most existing studies (see Subsections 1.3.2–1.3.4). The taxonomic status of the "Altai" saker falcon, also predominantly found in Russia, has long been debated (Karyakin, 2011), making it a critical study object.

Additionally, there is currently evidence of genetic differentiation among recognized saker falcon subspecies (Petrov et al., 2024) and some Asian populations (Pan et al., 2017; Hu et al., 2022). However, the genetic variability of South Siberian saker falcon populations remains unstudied. We hypothesize that their current phenotypic and genetic variability represents a remnant of the once-existing intraspecific structure of Asian saker falcons (Rozhkova et al., 2026). Nevertheless, we believe that genetic evidence of this subspecific differentiation may still be detectable through analysis of these southern Siberian populations.

The importance of genetic studies on Russian saker and gyrfalcon populations stems not only from the above reasons but also from contradictions between various studies. These inconsistencies appear at multiple levels of genetic research, from early mitochondrial DNA (mtDNA) studies to current whole-genome analyses. Regarding conflicting mtDNA topologies, the following discrepancies must be highlighted:
1. Gyrfalcon clustering as a basal monophyletic group in cytochrome *b* (*cytb*) analyses (Wink et al., 2004);
2. Merging of genetic diversity between saker falcon and gyrfalcon when analyzing the control region fragment (412 bp, including the conserved central domain) (Nittinger et al., 2007);
3. A star-shaped topology of gyrfalcon haplotypes, with the most common haplotype differing from sakers by only one substitution in a combined parsimony network (~1540 bp, including *cytb* fragment (298 bp) and control region domains I and II) (Johnson et al., 2007).

Notably, the presence of amino acid substitutions in cytochrome *b*, a key membrane protein of the cytochrome *bc*₁ complex responsible for electron transfer and proton gradient formation during oxidative phosphorylation (Esposti et al., 1993; Zhang et al., 1998), suggests possible molecular adaptation. This makes mtDNA variability studies relevant not only phylogenetically but also as a potential subject for functional genomics.

Similarly, the level of genetic differentiation based on microsatellite analysis varies across studies (Nittinger et al., 2007; Johnson et al., 2007; Dawnay et al., 2008; Dawnay et al., 2009; Belokon et al., 2022). Regarding whole-genome data, the phylogenetic position of the gyrfalcon relative to the saker falcon remains contradictory—it is considered either a sister taxon (Hu et al., 2022) or a descendant lineage (Zinevich et al., 2023).

Thus, this study is relevant not only for the fundamental understanding of speciation mechanisms and intraspecific diversity but also for the conservation of understudied yet threatened populations of species valuable to humans. Furthermore, investigating the genetic diversity of Russian saker and gyrfalcon populations helps resolve existing phylogenetic contradictions between these young species and provides a foundation for developing and implementing conservation strategies.

## Aims and Objectives
**Aim:** To describe and analyze the genetic diversity of poorly studied populations of the saker falcon *F. cherrug* and gyrfalcon *F. rusticolus*, and to reconstruct phylogenetic relationships within the *Hierofalco* group.

**Objectives:**
1. Characterize mtDNA variability (cytochrome *b*, tRNA-Thr, control region) in saker falcons and gyrfalcons, and reconstruct the history of mitochondrial haplogroup formation within the *Hierofalco* group.
2. Evaluate the historical and modern genetic structure of South Siberian saker falcon populations.
3. Clarify the phylogenetic position of "Altai" phenotype saker falcons.
4. Resolve contradictions regarding the phylogenetic relationships between Asian saker falcons and gyrfalcons.

## Scientific Novelty
This study presents the first integrated analysis of genetic data at different organizational levels—mtDNA, microsatellites, and single nucleotide polymorphisms (SNPs)—for two falcon species, the saker falcon and gyrfalcon, from understudied populations within the Russian Federation. Special emphasis is placed on South Siberian populations, as they are crucial for preserving the species' phenotypic and genetic diversity and have been subject to long-term monitoring (1999–2025). Comparing genetic diversity data with population dynamics has provided a novel perspective on intraspecific differentiation in the saker falcon before and after its demographic collapse.

mtDNA analysis has not only contributed to resolving existing contradictions regarding the gyrfalcon's phylogenetic position relative to the Asian saker falcon but also revealed potentially non-random variability in the *cytb* gene. Microsatellite analysis enabled the first assessment of the modern structure of South Siberian saker falcon populations relative to their probable historical differentiation. For the first time, genome-wide SNP analysis (RADseq) was used to clarify the phylogenetic position of the "Altai falcon." Whole-genome data also genetically confirmed, for the first time, the hypothesis that the gyrfalcon descended from the Asian saker falcon.

## Theoretical and Practical Significance
Studying speciation mechanisms using non-model, evolutionarily young species significantly contributes to evolutionary biology. The studied species group is particularly interesting due to the diversity of habitats they occupy and the likely presence of prezygotic barriers that maintain differentiation in sympatric zones. Our data advance the understanding of the evolutionary history of *Hierofalco* species.

mtDNA analysis clarified the history and evolutionary rate of mitochondrial haplogroups, including potential molecular adaptation processes. Microsatellite analysis demonstrated that the species-specific marker set (Hou et al., 2018) can be used to assess genetic structure in both wild saker and gyrfalcon populations. SNP analysis confirmed the conspecificity of the "Altai falcon" and Asian saker falcons, as well as the previously hypothesized recent divergence of the gyrfalcon.

Saker falcons and gyrfalcons are protected species, and active conservation efforts are underway (Kovács et al., 2014; Schneider et al., 2018; Red Book of Russia, 2021; Karyakin et al., 2022; Prommer et al., 2025). Therefore, genetic data on their threatened populations are valuable for conservation initiatives (reintroductions, monitoring, population genetic health assessments, etc.). This study underscores the critical importance of combining long-term monitoring with integrated genetic approaches in conserving threatened wild populations of rare species.

## Propositions Defended
1. The gyrfalcon is a descendant phylogenetic lineage of the Asian saker falcon.
2. Intraspecific differentiation in the historically widespread saker falcon, prior to its demographic collapse, was likely driven by prezygotic reproductive barriers. The genetic and phenotypic variability of modern South Siberian Asian saker falcons reflects both ancestral diversity and the consequences of anthropogenic population dynamics.
3. The "Altai" phenotype, specific to the Altai-Sayan region, is not genetically distinct within the Asian saker falcon's genetic variability.

## Reliability and Validation of Results
The results have been published in peer-reviewed journals. Their reliability is ensured by the use of established, widely validated methodologies. Specialized, certified equipment and reagents were employed for genetic data generation (see Chapter 2), including thermal cyclers (GeneExplorer, Veriti, SimpliAmp), genetic analyzers (3500 Genetic Analyzer, NanoPhor-05), a bioanalyzer (Bioanalyzer), and the Illumina HiSeq platform.

A sufficient sample size (222 individuals) was analyzed to ensure statistical robustness. Data processing utilized appropriate software: GeneMarker, SeqMan, MEGA, DnaSP, GenAlEx, Micro-Checker, Gimlet, Geneland, STRUCTURE, DAPC (in R-package adegenet), PopArt, HaplowebMaker, SWISS-MODEL, I-TASSER, PROVEAN, TreeSAAP, FigTree, and BEAST.

Research problems and interim results were presented at Russian and international conferences: (1) 25th Anniversary Conference of the Bird Conservation Union of Russia (Moscow, 2018); (2) 6th International Eurasian Ornithology Congress (Heidelberg, 2018); (3) Lomonosov-2018 Conference (Moscow, 2018); (4) 120th Anniversary of Prof. G.P. Dementyev Conference (Zvenigorod, 2018); (5) 2nd Int. Conf. "Eagles of the Palearctic: Study and Conservation" (Altai, 2018); (6) 18th Int. School-Conf. "Current Problems in Developmental Biology" (Moscow, 2019); (7) 8th Int. Conf. in Memory of A.I. Shepel (Voronezh Reserve, 2020); (8) International Saker Falcon Conference and Workshop (2021); (9) Young Scientists Conf. "Current Problems in Developmental Biology" (Moscow, 2021); (10) 29th All-Russian Youth Scientific Conf. (Syktyvkar, 2022); (11) 2nd All-Russian Ornithological Congress (St. Petersburg, 2023); (12) 7th Int. Buturlin Readings (Ulyanovsk, 2022); (13) Int. Seminar "Status and Conservation Problems of the Saker Falcon" (Almaty, 2023).

## Publications
The author has published 18 scientific works related to this dissertation, including three articles in peer-reviewed journals indexed in VAK, Scopus, and Web of Science.

## Personal Contribution of the Author
The author personally performed a substantial portion of the research. This included field collection of biological material—from museum specimens to participation in monitoring expeditions for saker falcons in the Altai-Sayan region (2018, 2021).

Laboratory work, including DNA extraction, PCR, fragment analysis, and Sanger sequencing, was conducted by the author. Specialized protocols (RADseq library preparation) were performed with direct author participation. Sequencing data analysis, fragment analysis, statistical processing, and literature-based interpretation were carried out independently by the author, except for bioinformatic RADseq data processing, which required specialized expertise.

The author's role in the articles Rozhkova et al., 2021 and Rozhkova et al., 2026 included formulating research aims and objectives, collecting and processing materials, and manuscript preparation. The author co-authored Zinevich et al., 2023, contributing to field sample collection, laboratory processing, result interpretation, discussion, and manuscript drafting. The dissertation was written entirely by the author based on original data collected independently or with direct participation.

## Structure and Volume of the Dissertation
The dissertation comprises ? pages and follows a traditional structure: introduction, literature review, materials and methods, results, discussion, conclusion, main findings, acknowledgments, list of author's publications, and references (? sources). Appendices add ? pages. The main text includes 8 figures and 8 tables; appendices contain 7? tables and 15? figures.

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# CHAPTER 1. LITERATURE REVIEW

## 1.1. Theoretical Foundations of Speciation

### 1.1.1. The Species Problem
Speciation is the evolutionary process by which new species arise. However, the definition and understanding of the term "species" remain highly debated, forming the essence of the "species problem" (Coyne & Orr, 2004; Pavlinov, 2009; Wilkins, 2009; Zachos, 2016; Sandberg et al., 2025). Essentially, contradictions in this field reflect the ongoing process of describing observed biodiversity, its structure, and the mechanisms driving it. Undoubtedly, a species, as a unit of biodiversity, is a complex and multifaceted phenomenon requiring both terminological definition and biologically sound description (Mayr, 1987, 1996). Consequently, dozens of species concepts have been formulated, each proposing frameworks for categorizing species, with all named entities treated as species (Zachos, 2016). Existing concepts can be divided into ontological and operational categories, describing either the theoretical essence of species or clear criteria for identifying them. Literature analyzing and critiquing species concepts is extensive (Mayr, 1987, 1996; Wheeler, Meier, 2000; Coyne & Orr, 2004; de Queiroz, 2007; Mallet, 2007; Wilkins, 2009; Harrison, 2014; Zachos, 2016; Fišer et al., 2018; Edwards et al., 2020; Hong, 2020; Sandberg et al., 2025). Below are the main concepts applicable to sexually reproducing organisms:

1. **Taxonomic or Morphological Species Concept**: Strictly operational, defining species based on distinguishing morphological traits (Blackwelder, 1967). Widely used by taxonomists despite reliance on expert subjectivity and lack of inherent "biological meaning" (Pavlinov, 2009).
2. **Biological Species Concept (BSC)**: Operational, defining species primarily by reproductive isolation under natural conditions and maintenance of a cohesive gene pool (Dobzhansky, 1937; Mayr, 1963). Limitations include difficulty measuring gene flow in nature, inapplicability to allopatric populations, and varying gene flow across genomic regions (Harrison, 2014).
3. **Phylogenetic or Genealogical Species Concept**: Operational, defining a species as a phylogenetic taxon characterized by monophyly (Baum, Shaw, 1995; Mishler, Theriot, 2000). Limitations include the rarity of true monophyly in nature and method-dependent detection (Mallet, 2007; Harrison, 2014).
4. **Genotypic Cluster Species Concept**: Operational, defining species as morphologically and genetically distinct groups that rarely or never produce intermediate forms upon contact. Genetically, this corresponds to identifiable clusters with heterozygote deficiency or non-random allele distribution (Mallet, 1995). Limitations: designed to statistically validate taxonomists' views, primarily applicable to sympatric populations (Mallet, 2007).
5. **Evolutionary Species Concept**: Ontological, defining a species as a single lineage of ancestor-descendant populations maintaining its identity from other lineages and possessing its own evolutionary tendencies and historical fate (Simpson, 1951; Wiley, 1978). Limitations: vague criteria, subjective application, and inability to delineate species across time (Mayr, 2000).
6. **Unified Species Concept**: Ontological, synthesizing other concepts by defining a species as a separately evolving metapopulation lineage (de Queiroz, 2007). It treats reproductive isolation, monophyly, etc., as properties that may emerge during divergence, not prerequisites. It emphasizes using multiple lines of evidence to demonstrate lineage separation. Limitations: lacks explicit diagnostic criteria, considered by some as overly broad (Pavlinov, 2009).

Currently, no "ideal" species concept exists that fully explains both the origin of species as biological entities and the phenomenon itself (Pavlinov, 2009). The scientific community now recognizes that while no single concept applies universally, each is useful depending on the study system (Mayr, 1996; Pavlinov, 2009; Harrison, 2014; Fišer et al., 2018; Sandberg et al., 2025).

A particular interest lies in delineating species undergoing divergence, i.e., accumulating species-specific traits (Coyne & Orr, 1989; Mayr, 1996; Matute & Cooper, 2021; Sandberg et al., 2025). Since this dissertation focuses on such species, selecting an appropriate species concept is essential. Considering the strengths and limitations outlined, we adopt the taxonomic concept for operational classification and the unified species concept for understanding biodiversity units. The latter was chosen because it accommodates allopatric and diverging populations and encourages searching for secondary diagnostic criteria reflecting accumulated differences (de Queiroz, 2007).

### 1.1.2. Reproductive Isolation
The species problem highlights potential mechanisms driving new species formation. Ultimately, speciation relies on the development of isolation, which prevents gene exchange between diverging populations (Dobzhansky, 1937; Coyne & Orr, 1989). Isolating barriers arise at different reproductive stages due to internal and external factors (Mayr, 1963; Coyne & Orr, 2004), classified as:
1. **Prezygotic**: Acting before or after mating but before zygote formation. Includes ecological, temporal, geographic, behavioral, and mechanical barriers (precopulatory), and gamete/female tract incompatibilities (postcopulatory).
2. **Postzygotic**: Acting after zygote formation. Includes zygote death, hybrid inviability, or hybrid sterility (Harrison, 2014).

Based on how reproductive isolation develops, several models are recognized:
1. **Allopatric speciation** (Dobzhansky, 1937; Mayr, 1963): Reproductive isolation arises due to geographic separation preventing gene flow (Jordan, 1905; Phillimore, 2014). Subtypes include:
   - *Vicariant*: Sister species with non-overlapping ranges formed by a geographic barrier; taxon age matches barrier formation.
   - *Peripatric*: Small founder populations colonize new areas, leading to minimal/no gene flow and rapid change due to small population size ("founder effect") (Phillimore, 2014).
2. **Sympatric speciation** (Maynard Smith, 1966): Reproductively isolated populations arise within the ancestral range despite continuous gene flow (Bolnick, Fitzpatrick, 2007; Phillimore, 2014).
3. **Parapatric speciation**: Occurs in adjacent or geographically separated populations with limited (non-zero, non-continuous) gene flow (Phillimore, 2014).

Genetic drift (Chetverikov, 1926), or "genetic-automatic processes" (Dubinin, 1986), significantly impacts isolated populations. During range fragmentation and population decline, drift reduces genetic diversity, increases inbreeding, and differentiates previously connected populations. Similar patterns were observed in small, isolated populations of Dupont's lark *Chersophilus duponti* (Méndez et al., 2011).

### 1.1.3. Natural Selection
Reproductive isolation results from natural selection, categorized into directional, disruptive, and stabilizing forms (Schmalhausen, 1946; Timofeev-Ressovsky et al., 1969; Endler, 1986). Directional and disruptive selection play major roles in speciation:
1. **Directional selection** favors extreme phenotypes, shifting the population mean. Likely primary in allopatric divergence with restricted gene flow, where selected alleles evolve faster than neutral regions.
2. **Disruptive selection** favors both extreme phenotypes over intermediates, potentially splitting populations. More likely to drive reproductive isolation in sympatry under high gene flow.

Stabilizing selection does not drive speciation but maintains differences between already diverged populations (Schmalhausen, 1946; Lowry, Hopkins, 2014).

**Sexual selection** also influences isolation by causing differential reproductive success based on trait expression (Fisher, 1930). It operates via:
1. **Intrasexual competition**: Same-sex individuals compete for mates (e.g., male-male combat, displays, courtship gifts).
2. **Intersexual choice**: One sex selects mates based on preferred traits (e.g., female choice), driving evolution of mating traits (Andersson, Iwasa, 1996; Boughman, 2014).

Sexual selection can establish precopulatory barriers where individuals from different populations no longer recognize each other as mates. Assortative mating (preference for similar phenotypes) can also occur (Jiang et al., 2013). Sexual selection significantly accelerates speciation (Boughman, 2014). Four mechanisms are recognized:
1. **Sensory drive**: Sensory systems evolve in response to environmental conditions, selecting mating traits that are easily perceived. Can cause precopulatory isolation upon secondary contact (e.g., Lake Victoria cichlids at different depths) (Seehausen et al., 2008; Boughman, 2014).
2. **"Good genes" model**: Females prefer males with traits indicating high local adaptation, producing fitter offspring. Drives divergence in sympatry when coupled with disruptive selection (van Doorn et al., 2009; Boughman, 2014).
3. **Fisherian runaway selection**: A genetic correlation between a male trait and female preference leads to rapid, self-reinforcing trait exaggeration until natural selection counteracts it (Fisher, 1930; Boughman, 2014).
4. **Sexual conflict**: Differing reproductive investments lead to antagonistic coevolution (e.g., male persistence traits vs. female resistance). Can drive adaptive radiation after habitat colonization (Gavrilets, 2000; Boughman, 2014).

Sensory drive and "good genes" models primarily affect sympatric subpopulations in heterogeneous environments, while runaway selection and sexual conflict operate independently of environment, potentially isolating allopatric populations through independent genetic trajectories. All four mechanisms accelerate speciation by creating non-random gene flow (Kraaijeveld et al., 2011; Boughman, 2014).

### 1.1.4. Hybridization and Its Role in Speciation
Gene flow levels determine whether diverging populations accumulate genetic differences. High flow homogenizes allele frequencies, while absent/rare flow allows independent evolution (Buerkle, 2014). When gene flow occurs between already diverged populations (even at the species level), it is termed hybridization (Barton & Hewitt, 1989; Buerkle, 2014).

Hybridization is common in nature and detectable genomically (Payseur & Rieseberg, 2016). Its evolutionary impact depends on isolation levels; young species hybridize more frequently (Mallet, 2005; Abbott et al., 2013). Outcomes vary (Abbott et al., 2013; Stankowski et al., 2021; Adavoudi & Pilot, 2022):
1. **Loss of divergence**: Secondary contact without isolation mechanisms can erase genetic differences via allele homogenization (e.g., ephemeral speciation in *Melidectes* honeyeaters, Müller et al., 2025).
2. **Hybrid zones**: Geographic areas where diverging populations interbreed, characterized by clines (gradients in allele/genotype/phenotype frequencies). Zones vary in width and structure. "Tension zones" balance dispersal and selection against hybrids (Barton & Hewitt, 1985, 1989; Harrison, 1993; Abbott et al., 2013; Buerkle, 2014). Hybrid inviability may follow Bateson-Dobzhansky-Muller incompatibilities (e.g., *Ficedula* flycatchers, Ålund et al., 2023).
3. **Reproductive isolation in hybrids**: Can lead to new species. Hybrid fitness may exceed, match, or fall below parental lines. In new habitats, hybrid traits may drive adaptive radiation. Chromosomally, hybrid speciation occurs via homoploidy (diploid hybrids isolated by ecology/space) or allopolyploidy (chromosome doubling causing instant isolation). Examples: *Heliconius* butterflies (homoploid), fish/tetrapods (allopolyploid), and extensively in plants (Abbott et al., 2013; Buerkle, 2014).

Incomplete pre/postzygotic isolation often leads to hybridization in birds (e.g., *Pica pica* subspecies, Kryukov et al., 2022; birds-of-paradise, Blom et al., 2024). Hybridization and introgression demonstrate the "semi-permeability" of species boundaries (Harrison, Larson, 2014). Introgression often affects genomic regions not under selection (Mallet, 2005), as seen in crow hybrid zones (*Corvus corone corone* vs. *C. c. cornix*), where plumage differences persist due to a selection-resistant "genomic island" (Poelstra et al., 2014). Thus, hybridization and introgression are evolutionarily significant speciation mechanisms.

### 1.1.5. Other Aspects of Speciation
Species interact with others (symbionts, parasites, prey, etc.), so speciation affects entire communities via coevolution (Thompson, 2014). An example is the Cassia crossbill *Loxia sinesciuris* population, isolated due to coevolution with lodgepole pine *Pinus contorta latifolia* in the absence of red squirrel competitors. Mutual "arms races" led to larger beaks, distinct vocalizations, and near-complete reproductive isolation (Benkman, 2010).

Phenotypic traits involved in precopulatory isolation can stem from various genetic mechanisms, from single SNPs to chromosomal rearrangements. For example, dark vs. blue-black plumage in the chestnut-bellied monarch *Monarcha castaneiventris* is controlled by a single non-synonymous SNP (Asp119Asn) in the *MC1R* gene. This dominant allele drives assortative mating and incipient speciation (Uy et al., 2009). Similarly, crow color differences persist despite introgression due to a genomic island on chromosome 18 containing pigmentation (*CACNG*) and vision (*RGS9*) genes under positive selection, driving assortative mating (Poelstra et al., 2014).

Postzygotic isolation mechanisms depend on type:
1. **Extrinsic/ecological**: Hybrids are maladapted to parental niches, showing intermediate traits under selection in parental populations.
2. **Intrinsic/physiological**: Developmental pathologies in hybrids. Causes include polyploidy, Bateson-Dobzhansky-Muller incompatibilities, Haldane's rule (sterility/inviability in heterogametic sex), and large X-effect (Orr, McNabney, 2014).

Postzygotic isolation acts at allelic and chromosomal levels. Genomic architecture (location of functional elements) critically influences speciation by affecting the origin and retention of genetic variation (Feder et al., 2014). Key processes include:
1. **Evolution of "speciation genes"**: e.g., *PRDM9*, regulating meiosis and recombination hotspots. Allelic differences cause hybrid sterility in house mice (Brick et al., 2012).
2. **Genomic islands of divergence**: Genomic regions with higher interspecific differentiation than neutral expectations. Size influenced by locus proximity, recombination rate, selection strength, and analytical methods. Identified in *Sporophila* seedeaters, linked to recent selective sweeps affecting melanin biosynthesis genes (Hejase et al., 2020).
3. **Genetic hitchhiking**: Allele frequency changes due to linkage with selected loci. "Divergence hitchhiking" reduces gene flow around selected loci. Under multifarious selection, "genome hitchhiking" reduces flow genome-wide, correlating adaptive divergence with genetic differentiation regardless of geography ("isolation by adaptation") (Nosil et al., 2009; Feder et al., 2012, 2014).

In summary, polyploidy and speciation genes drive postzygotic isolation during hybridization, while hitchhiking, genomic islands, and inversions prevent homogenization in early sympatric divergence. Genomic organization thus plays a crucial role in reproductive isolation and speciation.

## 1.2. Study Objects
The term *Hierofalco* (Cuvier, 1817) currently denotes a subgeneric/supra-specific group of diurnal falcons (genus *Falco*, family Falconidae): lanner *Falco biarmicus*, laggar *F. jugger*, black falcon *F. subniger*, saker *F. cherrug*, and gyrfalcon *F. rusticolus*. These falcons share morphological (body proportions, plumage structure, vocalizations) and ecological (open-habitat preference) traits and produce fertile hybrids (Eastham, Nicholls, 2005; Nittinger et al., 2005; Debus, Olsen, 2010; Wilcox et al., 2019). Genetic data confirm their grouping as a recently diverged evolutionary complex (Wink et al., 2004; Nittinger et al., 2007). Divergence from the sister species peregrine falcon *F. peregrinus* is dated to 1.8–1.2 Ma (Fuchs et al., 2015). Subsequent divergence likely involved range expansion and adaptation, reflected in their current allopatric distribution (Figures 1, 2, P1–P4, P6).

This study focuses on Russian saker and gyrfalcon populations, which are underrepresented in published literature. Below is a brief overview of all *Hierofalco* species to contextualize their relationships.

### 1.2.1. Lanner Falcon *Falco biarmicus* (Temminck, 1825)
Widely distributed across Africa and parts of the western Palearctic (e.g., Italy) (Figure P1) (BirdLife International, 2021). Leonardi (2017) recognizes five subspecies based on plumage and range: *F. b. biarmicus* (southern/southeastern Africa), *F. b. abyssinicus* (sub-Saharan tropics), *F. b. erlangeri* (Northwest Africa), *F. b. tanypterus* (Northeast Africa/Middle East), and *F. b. feldeggii* (Mediterranean). Most are resident or make intra-African movements; some undertake Palearctic migrations. Listed as Least Concern (IUCN), though declining. Included in CITES Appendix II.

### 1.2.2. Laggar Falcon *Falco jugger* (Gray, 1834)
Ecological counterpart to the lanner on the Indian subcontinent (Figure P2) (BirdLife International, 2020), despite geographic separation (Leonardi, 2017). Smallest in the group, resident, and monotypic. IUCN: Near Threatened (declining). CITES Appendix I.

### 1.2.3. Black Falcon *Falco subniger* (Gray, 1843)
Native to Australia (Figure P3) (BirdLife International, 2024). Ecologically and morphologically closest to the laggar. Characterized by uniformly dark plumage (brown to black) with variations. Shares behavioral and vocal similarities with other *Hierofalco* (Debus, Olsen, 2010; MacColl, Debus, 2022). IUCN: Least Concern (stable). CITES Appendix II.

### 1.2.4. Saker Falcon *Falco cherrug* (Gray, 1834)
Distributed across the Palearctic in open temperate habitats, primarily arid/semi-arid zones from Central Europe to the Far East: alpine belts, forest-steppe, steppe, semi-desert, and mountain desert zones (Figure 1, P4) (Kovács et al., 2014; BirdLife International, 2021).

Ecological plasticity is high: populations may be resident, nomadic, or migratory, using varied flyways and wintering grounds. Nesting behavior varies; e.g., a shift from cliff to tree nesting occurred in the Tuva Basin (Karyakin et al., 2018, 2022). This variability makes the saker a key phylogenetic study subject in the group.

#### 1.2.4.1 Current Taxonomic Status
High phenotypic/ecological variability led to debates over subspecies and the "Altai falcon" status (uniformly/partially dark individuals; Karyakin, 2011). Four subspecies are currently recognized: nominate *F. c. cherrug* (west), Turkestan *F. c. coatsi*, Tibetan *F. c. hendersoni*, and Central Asian *F. c. milvipes* (Clements et al., 2024; Gill et al., 2025). Alternative views on the "Altai falcon" are discussed in Section 1.3.

#### 1.2.4.2 Demographic Dynamics
Historically continuous, the range collapsed in the 20th century due to pesticides and human persecution, especially falconry (Nikolenko et al., 2014). Two main refugia remain:
1. Western: Central/Eastern Europe.
2. Eastern: Asia, from Turkey/Aral-Caspian to Dauria, including southern Siberia where Asian subspecies ranges overlap (Karyakin, 2011).

European populations survived as two isolated groups: Central European (Hungary, Slovakia, Serbia, etc.) and Eastern European (Ukraine, Moldova, E. Romania). Total ~400 pairs in 2012, recovering to 570–694 pairs by 2022. Despite growth, Central and Eastern European populations remain genetically isolated. Eastern European sakers formerly inhabited European Russia.

Eastern (Asian) populations declined less severely due to larger initial sizes and vast, sparsely populated habitats. The largest remaining Asian population is in the Altai-Sayan region (Galushin, 2005; Karyakin 2008; Kovács et al., 2014).

#### 1.2.4.3 Monitoring Data from South Siberian Populations
Long-term monitoring began in the Altai-Sayan region in 1999 alongside conservation efforts (Karyakin et al., 2004, 2010, 2014, 2018, 2022). Data revealed population dynamics and intraspecific diversity shifts.

Declines began in the mid-1990s, peaking critically in 2005–2007. Pre-2000s populations were stable and structured into three phenotypic groups resembling European (*cherrug*), Central Asian (*milvipes*), and Mongolian (*progressus*) types, plus geographic morphs *saceroides* and *altaicus* (Figure P5). The demographic collapse erased this structure. Only a small *cherrug* group persists on Minusinsk Basin cliffs. *cherrug* and *altaicus* phenotypes nearly disappeared elsewhere, while *progressus* and *saceroides* increased, alongside intermediate/indeterminate morphs. This likely resulted from interbreeding among formerly distinct subpopulations due to critically low densities or local extinctions (Karyakin, 2011; Nikolenko et al., 2014).

#### 1.2.4.4 Conservation Status and Threats
Major anthropogenic threats: electrocution on power lines; illegal removal of eggs/chicks/adults; trade; poisoning (primary/secondary from pesticides/lead); collisions; disturbance; shooting; nest destruction (Kovács et al., 2014).

In Russia, European population declines were driven by winter trapping in the Middle East for falconry, exacerbated by other anthropogenic pressures. For Asian Russia, illegal extraction for falconry remains the primary threat (Galushin, 2005; Karyakin, 2008). Over 20 years of monitoring in Altai-Sayan shows nearly a 50% decline. The pandemic temporarily boosted nesting pairs due to reduced legal/illegal trapping, highlighting the impact of poaching (Karyakin et al., 2022).

IUCN: Endangered. Red Book of Russia (2021): Category 1 (Critically Endangered). CITES Appendix II. Listed as "Especially Valuable Wild Animals" in Russian law.

### 1.2.5. Gyrfalcon *Falco rusticolus* (Linnaeus, 1758)
Circumpolar distribution, marginally entering northern taiga (Figure 2, P6) (BirdLife International, 2021). Inhabits rocky Arctic coasts, mountains, forest-tundra, and tundra with nesting sites. Largest *Hierofalco* species, monotypic, with color morphs from white to dark. Adults remain near breeding grounds or move south to avoid polar night; juveniles disperse widely. Winter strategies vary: some stay (hunting ptarmigan), others move to coasts/islands with open water, or migrate south. Movement driven by prey availability (ptarmigan, seabirds) (Potapov, Sale, 2005; Sokolov et al., 2017; Red Book RF, 2021).

Highly valued in falconry, suffering from illegal poaching (Galushin, 2005; Nikolenko, Karyakin, 2020). Kamchatka and adjacent Koryakia are major poaching hotspots (Lobkov et al., 2020).

IUCN: Least Concern (stable globally). CITES Appendix I. Red Book RF (2021): Category 2 (Vulnerable). Listed as "Especially Valuable Wild Animals."

## 1.3. Genetic Variability and Unresolved Taxonomic Issues of the Hierofalco Group

### 1.3.1. Systematics of Large Falcons Based on Non-Genetic Studies
Early researchers noted close relationships among large falcons. N.A. Severtzov (1855) suggested *F. candicans*, *F. islandicus*, *F. gyrfalco*, and *F. sacer* might be one species. M.A. Menzbier (1882) proposed an ancient origin, later establishing the genus *Hierofalco* in "Birds of Russia" (1895), including saker, Icelandic/Norwegian/Polar gyrfalcons, with sakers ranging from Morocco to the Upper Yenisei and India. He described *H. altaicus* (1891) and *H. lorenzi* (1900), initiating the "Altai falcon" taxonomic debate.

Otto Kleinschmidt (1901) first proposed all known forms belonged to a single "circle of forms" (*Falco Hierofalco*), including *islandus, gyrfalcon, uralensis, sacer, mexicanus, feldeggi, erlangeri, tanypterus, biarmicus, juggur, lorenzi,* and *altaicus*. Potapov & Sale (2005) interpreted this as an early phenotypic concept. Phenotypic diversity became a major taxonomic hurdle until genetic data emerged.

P.P. Sushkin (1915) studied Altai "Altai gyrfalcons," concluding they were transitional between *F. cherrug* (especially *F. milvipes*) and northern gyrfalcons. Later (1938), he treated *F. lorenzi* as a personal variation of highly variable *F. altaicus*.

M.A. Menzbier (1916) placed lanner in *Falco*, but grouped sakers under *Gennaia* (including Siberian, Tibetan, variegated, Altai, and Indian forms) and gyrfalcons under *Hierofalco* (Greenlandic, Icelandic, Norwegian).

G.P. Dementyev prioritized studying large falcon systematics and history. In his guide, he noted all saker/gyrfalcon forms are morphologically/ecologically similar, representing a continuous variation series. He emphasized the "Altai gyrfalcon" issue and noted uncertain relationships between sakers, laggar, and Mexican falcon. He distinguished European, common, Siberian, Turkestan, Mongolian, and Tibetan sakers. For gyrfalcons, he viewed them as typical "evarks" with size increasing from the North Atlantic to NE Asia/Greenland, except the smaller, distinct mountain Asian *F. g. altaicus*. He recognized Lapland, Siberian, East Siberian/Kamchatka, and Altai gyrfalcons. In a dedicated gyrfalcon monograph (1951b), he linked climate/metabolism to plumage, noting increased white morphs toward the pole. He considered the "Altai gyrfalcon" a melanistic, polymorphic boreo-alpine form. Initially agreeing they were one species with sakers, he later concluded large falcon differentiation predated glaciations, with modern forms emerging alongside the modern Arctic fauna or surviving glaciation in situ. He concluded differentiation split *Falco* into two groups: *F. peregrinus* (with weakly/strongly expressed subspecies) and the now species-level *F. gyrfalco, F. cherrug, F. biarmicus, F. jugger, F. mexicanus, F. subniger*.

A.F. Kots (1948), analyzing color phases, concluded all gyrfalcons are "color phases" of one species, forming a morph series. He hypothesized the "Altai gyrfalcon" resulted from hybridization between saker and Norwegian gyrfalcon.

L.S. Stepanyan (1990) recognized *Hierofalco* as a superspecies group: Palearctic *F. cherrug, F. rusticolus*, Nearctic *F. mexicanus*, Indo-Malayan/Palearctic *F. jugger*, with possible inclusion of *F. biarmicus*. He recognized two gyrfalcon races in the USSR and four saker subspecies.

Later, R. Pfeffer (2009) proposed eight saker subspecies. I.V. Karyakin (2011), using spatial phenotypic analysis, concluded western sakers are uniform, while eastern sakers include at least five distinct races. He reviewed the *F. altaicus* issue extensively, concluding "Altai falcons" result from western-eastern saker hybridization, forming a distinct phenotype group in a narrow contact zone at the Russia-Mongolia border. Others consider them conspecific with sakers due to lack of genotypic/phenotypic cohesion (Koblik, Arkhipov, 2014).

Foreign views evolved similarly: from including *F. mexicanus* in *F. rusticolus* (Meinertzhagen, 1954), to questioning the grouping (Vaurie, 1961), to supporting a superspecies concept (Stresemann, Amadon, 1979). Vaurie (1961) recognized two saker subspecies (*cherrug, milvipes*) based on clinal color variation, treated *F. altaicus* separately, and rejected gyrfalcon subspecies due to clinal grading. Stresemann & Amadon (1979) added *F. (cherrug) altaicus* as a third subspecies, recognized four gyrfalcon and five lanner subspecies. Later works maintained uncertainty, recognizing two saker subspecies, no gyrfalcon subspecies, and ambiguous "Altai falcon" status (Forsman, 1999).

Morphological/ecological studies built the *Hierofalco* concept, heavily influenced by Russian researchers due to extensive ranges in Russia/USSR. Limitations included adaptive convergence and insufficient data. Genetic studies subsequently elevated taxonomic debates.

### 1.3.2. Studies of Mitochondrial DNA Variability in the Hierofalco Group
Early molecular studies focused on mtDNA, widely used in phylogenetics and other applications (Harrison, 1989; Kowalczyk et al., 2021). Bird mtDNA gene order differs from other vertebrates (Mindell et al., 1998). In saker/gyrfalcon, the order is: *ND5, cytb, tRNA-Thr, Control Region (CR), tRNA-Pro* (Lu et al., 2016; Sveinsdóttir et al., 2017), likely conserved across *Hierofalco*.

*cytb* encodes a key complex III protein for oxidative phosphorylation. Its conservatism suits phylogenetics and molecular clocks, but low mutation rate and nuclear copies (NUMTs) limit intraspecific utility (Meyer, 1994; Stanley, Harrison, 1999; Nacer, do Amaral, 2017).

Early *Falco* phylogenies using *cytb* (300 bp) supported *Hierofalco* but later were corrected for NUMTs (Wink, Sauer-Gürth, 2000; Wink et al., 2004). True mt *cytb* (>1000 bp) confirmed *Hierofalco* as monophyletic, young, and sister to *F. peregrinus*. Expanded *cytb* analyses showed black falcon likely belongs to the group, saker has highest diversity (three clades not matching geography/phenotypes), "Altai falcons" lack genetic distinctness, and divergence occurred 200 kya–1 Ma. Full *cytb* (1143 bp) confirmed early divergence stages, with *F. rusticolus* forming a distinct clade and *F. ch. cherrug/milvipes* grouping with *F. b. feldeggii* (Wink, 2018). A large-scale gyrfalcon study (165 samples) found only four *cytb* polymorphisms (Johnson et al., 2007).

The Control Region (CR/D-loop) is hypervariable, accumulating mutations faster, ideal for young species/population studies. Limitations include VNTRs, indels, heterogeneous mutation rates, and NUMTs (Ruokonen, Kvist, 2002). CR structure in sakers includes 5'/3' repeats, poly-C stretch, ETAS1, conserved boxes (E, D, CSBa/b/1), and termination/replication sites. "Goose hairpin" motifs are common in birds.

Foundational CR studies by Nittinger et al. (2005, 2007) analyzed 418 bp CR fragments across 56 *Hierofalco*, revealing 31 haplotypes splitting into Clusters A (all species) and B (*F. cherrug, F. biarmicus*), supporting an African origin hypothesis with Pleistocene Palearctic colonization. Later (2007), 412 bp CR analysis of 200 samples revealed 97 polymorphic sites, 87 haplotypes. Cluster A's central haplotype (H-69) was universal. Cluster B contained only saker/lanner haplotypes. Gyrfalcons showed low diversity. Sakers from the west had more Cluster B, east more Cluster A. "Altai falcon" status was rejected. Results supported recent asymmetric mtDNA introgression from gyrfalcon to saker, with European populations showing bottleneck signatures. Modern haplotype distribution reflects incomplete lineage sorting and ancient/recent hybridization.

Johnson et al. (2007) combined *cytb*, tRNA-Thr, and CR (~1540 bp), finding 11 saker and 8 gyrfalcon haplotypes. Saker haplotypes formed two clusters; gyrfalcon formed a star topology around one dominant haplotype differing from a saker haplotype by one substitution. Authors proposed saker diversity resulted from secondary contact of isolated refugial populations, while gyrfalcons recently diverged via founder effect.

Recent studies on European lanner *F. b. feldeggii* using CR fragments (360 bp, 295 bp) confirmed two clusters independent of subspecies (Sarà et al., 2019; Attili et al., 2023).

In summary, mtDNA phylogenetics confirmed the young *Hierofalco* complex, identified two main haplogroups (A, B), showed sakers possess both while gyrfalcons only A, and confirmed "Altai falcons" lack unique mtDNA, likely representing a morph.

### 1.3.3. Studies of Microsatellite Locus Variability in the Hierofalco Group
Microsatellites (STRs/SSRs) are highly polymorphic nuclear markers useful for population structure, parentage, and hybrid identification (Galinskaya et al., 2019; Martínez-Cruz, Camarena, 2018).

First developed for peregrine falcons (Nesje et al., 2000), then gyrfalcons (Nesje, Roed, 2000). Johnson et al. (2007) used 8 loci, finding 45 gyrfalcon/47 saker alleles (13 saker-specific). Significant differentiation found among island gyrfalcon populations and continental birds. Russian samples absent. Nittinger et al. (2007) used 6 loci on 240 *Hierofalco* (186 sakers), finding no clear geographic differentiation but clustering sakers, gyrfalcons, and lanner populations separately by allele frequencies.

Downey et al. (2008) tested 9 loci for species ID (19 wild/16 captive gyrfalcons, 17 wild/20 captive sakers), achieving 98% accuracy at K=2. Eight loci later used on Russian gyrfalcons (Chukotka-Kamchatka), showing high polymorphism and suitability for ID (Nechaeva et al., 2018a).

Other studies used non-specific loci for Czech saker/peregrine diversity (Bryndová et al., 2012), individual ID from molted feathers (Dixon et al., 2016), and confirmed "Altai falcon" as a saker morph (Nechaeva et al., 2018b). Belokon et al. (2022) validated a 15-locus panel for captive ID.

European lanner *F. b. feldeggii* studies using 10–12 loci showed genetic differentiation from other lanner subspecies and European sakers, with no hybridization signals, confirming nuclear distinctness despite limited gene flow (Sarà et al., 2019; Attili et al., 2023).

Species-specific microsatellites for sakers were developed from reference genomes (Hou et al., 2018). Tested on 272 Mongolian saker feathers, they outperformed cross-species markers in polymorphism and parentage assignment. Later used to confirm *F. c. cherrug* vs. *F. c. milvipes* in Bulgarian captive populations (Petrov et al., 2024) and assess relatedness in rehabilitation centers (Petrov et al., 2023).

In summary, microsatellite analyses revealed genetic differentiation among *Hierofalco* species, intraspecific structure in lanner/gyrfalcon, Mongolian saker diversity, Chukotka-Kamchatka gyrfalcon diversity, and lack of "Altai falcon" distinctness. Results depend on marker number, polymorphism, specificity, and sample size. Microsatellites remain valuable for conservation/forensic applications, though results often contrast with mtDNA findings.

### 1.3.4. Other Molecular Genetic Studies of the Hierofalco Group
Falcons exhibit reduced chromosome numbers (2n=40–52) vs. ancestral avian karyotype (~2n=80) due to fusions and microchromosome loss (Nishida et al., 2008; Wilcox et al., 2022). Saker/gyrfalcon karyotypes are identical (2n=52) (Joseph et al., 2018). Linked-read sequencing of four *Hierofalco* genomes improved saker assembly, produced the first lanner genome, revealed GC-content imbalance from microchromosome loss, and showed genomes in constant flux. ML phylogeny placed lanner basal, then saker, then gyrfalcon. Divergence times: peregrine-*Hierofalco* ~588 kya, lanner-saker ~304 kya, saker-gyrfalcon ~141 kya (Wilcox et al., 2022). These contradict earlier estimates (1.8–1.2 Ma) from 8 loci + fossil calibrations (Fuchs et al., 2015), which analyzed mtDNA + 7 nuclear loci. Nuclear loci showed high shared alleles, explained by ancestral polymorphism/ILS rather than hybridization. mtDNA confirmed black falcon monophyly. Authors proposed rapid *Falco* radiation linked to Late Miocene/Pliocene C4 grassland expansion and migration evolution.

Next-Generation Sequencing (NGS) revolutionized nuclear DNA studies, enabling SNP discovery across genomes for phylogenetics/adaptation studies (Leaché, Oaks, 2017; Martínez-Cruz, Camarena, 2018). NCBI (2026) hosts reference genomes for saker, gyrfalcon, lanner, and laggar.

Zhan et al. (2013) compared saker/peregrine genomes, confirming rapid phenotypic evolution in Falconidae. Sakers showed adaptations in circulatory/nervous systems, olfaction, sodium transport, beak development, and heat stress homeostasis.

Zhan et al. (2015) analyzed 173 sakers globally (excl. Central Asia/Russia), identifying 144 SNPs across 12 fragments. Exonic SNPs differentiated Qinghai-Tibet Plateau (QTP) populations from others, suggesting selection on genes like *RPL13, COE2, MHC*. Central European sakers showed isolation signatures, with gene flow mediated by Central Eurasian populations.

Pan et al. (2017) sequenced 30 saker transcriptomes (10 QTP, 20 non-QTP), identifying 377,530 SNPs. QTP, Eastern, and Western populations diverged. Saker origin estimated at 34 kya, peak population 8.5 kya, followed by decline. East-West divergence ~2 kya. 37 SNPs under selection in QTP vs. Eastern involved hypoxia response (*EPAS1, Hemoglobin alpha, LDB1*) and immunity. 267 SNPs under selection in East-West comparison involved oxygen transport/hemoglobin binding. QTP sakers show higher *EPAS1* expression, enhancing oxygen utilization.

Hu et al. (2022) sequenced 40 full genomes (30 sakers west/east, 10 gyrfalcons Arctic Russia). Confirmed clear differentiation. Demographic modeling suggested divergence ~300 kya. Gyrfalcons and Asian sakers share >21.3% autosomal/25.4% Z-chromosomal alleles vs. 0.2%/0.0001% with European sakers. Asymmetric gene flow from gyrfalcon females to Eastern sakers confirmed (f3=-23.96). Hybridization dated to 17.5–10 kya in southern Siberia during Last Glacial Maximum. Saker expansion to East Asia ~78–38 kya, QTP colonization 12–8 kya. ABBA-BABA tests identified five genomic islands (>200 kb) with adaptive introgression on chr 1, 3, 5, 8, 16. *SCMH1* intron 5 showed introgressed SNPs in a cis-regulatory element, likely affecting body size. Other size-related genes (*HMGA2, MSRB3, LEMD3, FBXL15, NFKB2*) formed TADs. *SCARB1* introgression (Pro121Leu) likely enhanced HDL absorption, aiding cold adaptation. QTP adaptation to hypoxia involved selective sweeps on chr 4 (~500 kb, 293 SNPs) near hemoglobin genes (*HBZ, HBAD, HBA1*), altering chromatin accessibility and increasing *HBA1.2* expression. Darker QTP plumage linked to reduced *ASIP* expression via a cis-regulatory variant, increasing eumelanin. Authors concluded gyrfalcon introgression provided cold-adaptation variants (larger size, lipid metabolism), while regulatory changes enabled rapid QTP colonization.

In summary, nuclear DNA variability confirms the *Hierofalco* complex. Karyotypes are identical despite ongoing genomic flux, supporting rapid radiation (Fuchs et al., 2015), though divergence timing varies by method (Zhan et al., 2013; Fuchs et al., 2015; Wilcox et al., 2022). Phylogenies remain inconsistent, especially regarding saker-gyrfalcon divergence and saker population structure. Studies show European sakers are ancestral to Asian sakers, which colonized QTP (Hu et al., 2022). SNPs revealed adaptive elements, particularly in QTP sakers, and supported gyrfalcon descent from Asian sakers.

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