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By taking into account only the nucleotide misincorporations originally derived from A and T nucleotides, we observed that type 1 (A→G/T→C) transitions are the most represented in both the modern and ancient datasets.
On the other hand, when the nucleotide misincorporations originated from an underrepresented A and T nucleotide, their values were multiplied by the ratio G+C/A+T in the specific fragment The total number of the nucleotide misincorporation types observed within modern and ancient datasets were obtain by the sum of the nucleotide misincorporation number revealed in each group of clones.
The Hg frequencies within the ancient datasets were compared to those in modern Scandinavian dogs [ 9] using χ2 tests.
No isolation by distance was detected in any of the ancient datasets tested (or the combined modern and ancient datasets for either gene), most likely because while the modern dataset represents a snapshot in time, the ancient samples come from a very wide time range, and so patterns of isolation by distance may be obscured.
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As a result, 51 individual city-level population counts in Modelski's Ancient Dataset were omitted (Data Citation 2: FigShare http://dx.doi.org/10.6084/m9.figshare.org/10.6084/m9.figshare
Considering only the ancient dataset, we calculated 845.74 type 1 and 6530.17 type 2 transitions (type 1: type 2 ratio ∼1∶8), demonstrating that type 2 transitions represent the majority (85%) of the total observed misincorporations.
The complementary groups A→G/T→C, A→T/T→A (Figure 3B) are more frequent in the modern than the ancient dataset, while the complementary group C→T/G→A is more frequent in the ancient than the modern dataset (Figure 3A).
We observed that some complementary groups such as A→C/T→G, C→A/G→T transversions and C→T/G→A transitions are more frequent in the ancient dataset than in the modern, while A→T/T→A, C→G/G→C transversions and A→G/T→C transitions are more abundant in the modern dataset.
Interestingly, while Hg C is overrepresented in our ancient material, there is a complete lack of the Scandinavian group D in our ancient dataset.
Lastly, the χ2 test between the Hg frequencies of the complete ancient dataset with that of the complete Scandinavian (not only considering native breeds) demonstrated a significant deviation between the modern and ancient frequencies (p < 0.0388, χ2 = 4.27, df = 1).
When the complete ancient dataset was compared to the contemporary dataset, it proved equally improbable (p < 0.001) that Hg D was present in the oldest specimens in a frequency similar to that observed in modern dogs.
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CEO of Professional Science Editing for Scientists @ prosciediting.com