Siberian Husky Genetics
A Yukaghir nomadic family along the Korkodon River, Siberia, circa 1900. Published by the American Museum of Natural History Library. Original photograph by Waldemar Jochelson (1855–1937), taken during the Jesup North Pacific Expedition (1897–1902).
Credit: Waldemar Jochelson
Revealing the Complex Genetic Ancestry of the Yakutian Laika
By: Tracy Smith, PhD
Summary
The Yakutian Laika is an ancient sled dog breed native to the Sakha Republic (Yakutia) in northeastern Siberia, traditionally used by Indigenous peoples for transportation and hunting in harsh Arctic conditions. Following a dramatic population decline, the Yakutian Laika was the focus of concerted revival efforts beginning in the late 20th century, aimed at restoring the breed from near extinction. In this study, I analyzed the DNA of 37 modern Yakutian Laika dogs to explore their genetic relationship to the ancient Zhokhov dog — a 9,500-year-old Arctic sled dog regarded as one of the earliest known examples of domesticated dogs in the Arctic — and to assess the degree of European breed influence that may have shaped its contemporary genome.
The findings show that while the Yakutian Laika still retains some of its ancient sled dog heritage, its genetic makeup tells a more complex story. When comparing the DNA of Arctic breeds, the Yakutian Laika sits closer to European dog breeds like German Shepherds and Golden Retrievers than to other Arctic sled dogs such as the Greenland Dog, Malamute, or Siberian Husky (Figure 1). This suggests that the Yakutian Laika has experienced significant historical mixing, or admixture, with European breeds over time.
When looking for ancient ancestry from the Zhokhov dog—a 9,500-year-old Arctic sled dog—it was found that Greenland Dogs are most closely related to this ancient sled dog sharing ~86% of its ancestry, followed by Alaskan Malamutes (59%) and Siberian Huskies (36-41%). In contrast, the Yakutian Laika exhibited a much lower proportion of Zhokhov ancestry, around 8%, which was not statistically significant (Figure 2). Recent studies have shown that Siberian Huskies descend from a distinct lineage that diverged from the Greenland Dog population near the end of the Pleistocene, over 10,000 years ago (Smith et al., 2024). It is possible that the Yakutian Laika shares a greater proportion of its ancestry with this secondary Arctic dog lineage, which could account for its reduced affinity to the ancient Zhokhov lineage and its more complex genetic profile.
Further analysis showed that the Yakutian Laika has about 40% European ancestry, which is much higher than what we see in Malamutes or Siberian Huskies (Figure 3). This European influence appears throughout the Yakutian Laika population, not just in a few individuals, suggesting widespread historical mixing (Table 1).
In comparison, Greenland Dogs and many Siberian Huskies have remained more genetically isolated and retain stronger ties to ancient Arctic dogs, with little to no European admixture.
In summary, the Yakutian Laika is a fascinating breed that combines ancient Arctic sled dog roots with more recent European influence. This mix likely reflects a long history of human migration and trade in northern Siberia, where native dogs crossed paths and interbred with dogs brought by Soviet and European settlers. Some of this mixing may have also happened during more recent efforts to revive the breed. While the Yakutian Laika still shows some physical traits of its sled dog ancestors, its DNA tells a much richer story — one shaped by both isolation and new connections over time.
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Population Structure and Admixture Patterns
Principal component analysis (PCA) (Figure 1) shows that the Yakutian Laika is genetically distinct from the primary Arctic sled dog populations, including Greenland Sled Dogs, Malamutes, and Siberian Huskies. While the latter form three distinct clusters away from European breeds, the Yakutian Laika is displaced toward the European dog cluster. This pattern is supported by the TreeMix maximum likelihood tree (Figure 2), which places the Yakutian Laika as a sister lineage to the clade of European breeds, rather than clustering it with other Arctic sled dogs or the ancient Zhokhov lineage. The placements suggest that the Yakutian Laika may derive from a genetically divergent lineage with closer affinities to West Eurasian dogs. Together, these results indicate that the Yakutian Laika has experienced substantial European admixture, setting it apart from more genetically isolated Arctic sled dog breeds.
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Figure 1: Principal component analysis (PCA) of genetic variation among Arctic and European dog populations. Each point represents an individual, colored by population assignment. Principal components 1 and 2 explain 15.2% and 13.9% of the total genetic variance, respectively. The four Siberian Husky populations (Show, Racing, Pet, and Seppala) cluster closely, reflecting shared ancestry, whereas the Yakutian Laika is positioned closer to European breeds, consistent with historical gene flow.
Figure 2: Maximum likelihood tree inferred using TreeMix showing the relationships among ancient, Arctic, and European dog populations, rooted with the wolf outgroup. Branch lengths are proportional to genetic drift, with the scale bar representing 10 standard errors. Notably, the Yakutian Laika forms a sister lineage to the clade of European breeds (e.g., German Shepherd, German Shorthaired Pointer, Golden Retriever), rather than clustering with other Arctic sled dogs or the ancient Zhokhov lineage.
Zhokhov Ancestry Proportions
f4-ratio statistics estimating Zhokhov ancestry (Figure 3), a 9500-year-old sled dog found in the northeast Arctic Siberia, further highlight the Yakutian Laika’s distinct ancestry profile. Greenland Dogs showed the highest Zhokhov ancestry proportion at ~85.8% (Z-score = 19.031), followed by Malamutes (~58.9%, Z-score = 15.153) and Siberian Huskies from Show (~40.8%, Z-score = 12.404) and Racing lines (~36.5%, Z-score = 12.079). The Chukotka sled dog (CSD) also had a significant Zhokhov ancestry proportion at ~33.7% (Z-score = 11.272).​​
In contrast, the Yakutian Laika had a much lower Zhokhov ancestry estimate of ~7.9% (Z-score = 2.597), which was not statistically significant at the conventional Z ≥ 3 threshold. This low level of Zhokhov ancestry suggests that although the Yakutian Laika may retain some genetic legacy from ancient Arctic dogs, this signal has been diluted, likely due to subsequent gene flow events. Similarly, the Samoyed also showed a low and non-significant Zhokhov ancestry estimate of ~2.8% (Z-score = 0.596).
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A predicted phenotypic reconstruction of the ancient Zhokhov sled dog based on genotypes at various coat color and other trait loci from Smith et al. 2024.
Figure 3: Estimated proportion of Zhokhov ancestry in modern dog populations based on F4-ratio statistics. Each bar represents the proportion of ancestry attributed to Zhokhov, an ancient Arctic dog, with error bars indicating standard error. Populations with Z-scores ≥ 3 are considered statistically significant and are shown in blue; non-significant results (Z-score < 3) are shown in gray. Greenland Dogs exhibit the highest proportion of Zhokhov ancestry (~86%), followed by Malamutes (~59%) and Siberian Husky subpopulations (Show and Racing lines). Lower but significant proportions are observed in Chukotka sled dogs (CSD), while East Asian, Yakutian Laika, and Samoyed show low and non-significant levels of Zhokhov ancestry.
Figure 4: Estimated proportion of European ancestry in modern dog populations based on F4-ratio statistics. Bars represent the estimated ancestry proportion, with error bars indicating standard error. Populations with Z-scores ≥ 3 are considered statistically significant (blue), while non-significant results (Z-score < 3) are shown in gray. European breeds (Golden Retriever, German Shorthaired Pointer, German Shepherd) exhibit the highest proportion of European ancestry (~1.09), followed by the Samoyed and Yakutian Laika breeds. Lower but significant proportions are observed in Chukotka sled dogs (CSD), Malamutes, and Racing-line Siberian Huskies. Show-line Siberian Huskies display the lowest and non-significant levels of European ancestry.
European Ancestry Proportions
The analysis of European ancestry proportions based on f4-ratio statistics (Figure 4) provided complementary insights. European domestic dogs (Golden Retriever, German Shorthaired Pointer, German Shepherd) unsurprisingly had the highest European ancestry estimate of ~109.3% (Z-score = 18.324), serving as the reference point.
Among Arctic breeds, the Yakutian Laika showed a European ancestry estimate of ~40.5% (Z-score = 11.543), which was highly statistically significant. This proportion is higher than that found in Malamutes (~12.8%, Z-score = 4.248), Chukotka sled dogs (~24.3%, Z-score = 7.999), and Racing-line Siberian Huskies (~10.8%, Z-score = 3.929). The Samoyed exhibited an even higher European ancestry proportion (~50.1%, Z-score = 10.183), consistent with historical admixture with European dog lineages and reflecting their past geographic proximity to Europe. In contrast, the Show-line Siberian Huskies exhibited a very low and non-significant European ancestry estimate of ~3.1% (Z-score = 0.960).
These results align closely with the PCA findings, reinforcing the notion that the Yakutian Laika has received a substantial contribution from European dog lineages.
What is a Z-Score?
In science, Z-scores are used to tell us how unusual a measurement or result is compared to what we would expect if everything were “normal” or random.
Think of it like this: when researchers collect data, they usually assume there’s a general pattern — like most people’s blood pressure falls within a certain range. The mean (average) tells us the center of this range, and the standard deviation tells us how spread out the data are. The Z-score measures how far a particular observation is from the mean in terms of standard deviations.
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In scientific research:
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A Z-score of 0: Completely average — exactly what you’d expect.
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A Z-score of 2: About 95% of all results are closer to the mean than this. It’s still within the range of normal variation, but starting to get interesting.
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A Z-score of 3: Very unusual — less than 0.3% chance it happens randomly (p ≈ 0.003). In many fields, this is considered statistically significant evidence that something is going on.
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A Z-score of 5: Extremely unusual — about 1 in 3.5 million chance.
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A Z-score of 10: This would be astronomically rare — the chance of something happening this far from the mean just by luck is virtually zero.
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Testing for European Gene Flow
D-statistics (Figure 5) offer additional evidence of European gene flow into the Yakutian Laika. These statistics test for asymmetrical allele sharing between Greenland Dogs and the test populations relative to European breeds, using the Grey Wolf as an outgroup. A negative D-value indicates that the test population shares more alleles with European breeds than with Greenland Sled Dogs, signaling likely admixture with European breeds.
For the Yakutian Laika, the D-statistic was -0.067 (Z-score = -12.036), indicating a significant excess of European ancestry compared to Greenland Sled Dogs. This negative D-value for the Yakutian Laika was among the strongest observed across Arctic breeds, stronger even than in Malamutes (D = -0.0264, Z-score = -5.015) and Chukotka sled dogs (D = -0.0579, Z-score = -10.748). In contrast, Racing and Show-line Siberian Huskies exhibited non-significant D-values (-0.0131, Z-score = -2.949 for Racing and -0.0031, Z-score = -0.62 for Show), suggesting little to no excess European ancestry in these lines relative to Greenland Sled Dogs.
Figure 5: D-statistics testing for asymmetrical allele sharing between Greenland Dogs and modern Arctic dog populations relative to European dogs, using grey wolf as an outgroup. Bars represent D-statistic estimates, with error bars indicating standard error. Populations with |Z|-scores ≥ 3 are considered statistically significant (blue), while non-significant results are shown in gray. Negative D-statistics indicate excess allele sharing between the tested population and European dogs relative to Greenland Sled Dogs. Significant negative D-values were observed for Yakutian Laika, Chukotka sled dogs (CSD), and Malamutes, suggesting higher European ancestry compared to Greenland Sled Dogs, while Racing and Show-line Siberian Huskies exhibited non-significant results.
Testing Individual Dogs for European Gene Flow
Individual-level D-statistics further reinforced the population-wide signal of European admixture in the Yakutian Laika. Every individual tested displayed significantly negative D-values, with estimates ranging from -0.042 to -0.1196 and corresponding Z-scores between -4.482 and -10.378, providing strong evidence of gene flow from European breeds (Table 1). The consistency of this pattern across all sampled individuals indicates that European admixture is a pervasive characteristic of the Yakutian Laika genome rather than an artifact of a few outliers. In contrast, the Greenland Sled Dog and certain populations of the Siberian Husky do not exhibit similar signatures of European gene flow, instead retaining a greater proportion of their ancient Arctic genetic ancestry (Smith et al., 2024).
Table 1: D-statistics of the form D(W, X; Y, Z) testing allele frequency asymmetry between Greenland Dogs (W) and individual Yakutian Laika (X) relative to European breeds (German Shorthaired Pointer, German Shepherd and Golden Retriever) (Y), with Grey Wolf as the outgroup (Z). Negative D values indicate excess shared derived alleles between the Yakutian Laika individual and European dogs compared to Greenland Sled Dogs. The table reports the D-statistic (D), block jackknife standard error (stderr), Z-score (Zscore), counts of BABA and ABBA site patterns, and the total number of SNPs analyzed (nsnps). Significant deviation from zero (|Z| ≥ 3) provides evidence of gene flow between Yakutian Laika individuals and European breeds.
Conclusions
Collectively, these results reveal a complex demographic history for the Yakutian Laika. Although it retains some elements of its ancient Arctic dog ancestry, the breed has undergone substantial admixture with European dogs, as evidenced by its intermediate position in close proximity to European breeds in the PCA and phylogenetic tree, low Zhokhov ancestry proportion, high European ancestry proportion, and strongly negative D-statistics.
The relatively low proportion of ancient Zhokhov ancestry combined with significant European admixture sets the Yakutian Laika apart from more genetically isolated Arctic dog populations, such as the Greenland Dog and Siberian Husky, which have retained higher levels of ancient Arctic ancestry and show minimal European influence. These results suggest that the genetic profile of the Yakutian Laika has been shaped by historical interactions between Indigenous Arctic communities and Soviet or West Eurasian settlers, as well as possible intentional or unintentional crossbreeding with European dogs during 20th-century revival efforts. As a result, the Yakutian Laika represents not a direct genetic continuation of ancient Arctic sled dogs, but rather a modern derived lineage — a breed whose history is a testament to both its deep Arctic roots and the complex legacy of human-mediated animal movement and breed restoration.
References: Smith, T.A., Srikanth, K. and Huson, H.J., 2024. Comparative population genomics of Arctic sled dogs reveals a deep and complex history. Genome Biology and Evolution, 16(9), p.evae190.