1. Patterns of Genetic Coding Variation in a Native American Population before and after European Contact 
John Lindo, Mary Rogers, Elizabeth K. Mallott, Barbara Petzelt, Joycelynn Mitchell, David Archer, Jerome S. Cybulski, Ripan S. Malhi, Michael DeGiorgio 
The American Journal of Human Genetics 
Volume 102, Issue 5, Pages (May 2018)
DOI: /j.ajhg
Copyright © 2018 American Society of Human Genetics Terms and Conditions

2. Figure 1 Admixture Signal between the Modern Tsimshian and Europeans
TreeMix60 graph with a single admixture event. Admixture39 bar plots are shown to the right of each population, assuming K = 8 clusters. In the Prince Rupert Harbour (PRH) Ancients, the oldest individual (939) is depicted by the leftmost bar in the Admixture bar plots and shows a different ancestry pattern than the younger individuals.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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3. Figure 2
Predictive Damaging CADD Scores Harbored in C→T and G→A Transitions
Results indicate that transitions due to potential post-mortem deamination cannot account for the differences in CADD scores.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
Copyright © 2018 American Society of Human Genetics Terms and Conditions

4. Figure 3 Estimated Heterozygosity through Time
The ancient individuals are color-coded according to their burial sites. Shuká Káa is an ancient individual from present-day Alaska, which dates to approximately 10,300 calendar years BP.30 The plot also includes individual 938 (Lucy site, dating to approximately 5,670 calendar years BP), which is described in Cui et al.24
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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5. Figure 4 Derived Allele Frequency Spectra
Histograms depict the synonymous (A) and nonsynonymous (B) derived allele frequency spectra of the ancient and modern individuals.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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6. Figure 5
Excess of Potentially Functional Variants in the Ancient Individuals
(A) Ratio of nonsynonymous to synonymous changes in the ancient and modern individuals for variants grouped by minor allele frequency.
(B) Mean scaled CADD score of the functional changes for each frequency class in the ancient and modern individuals.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
Copyright © 2018 American Society of Human Genetics Terms and Conditions

7. Figure 6 CADD Classification of Functional SNPs in Each Population
The modern individuals show a reduced proportion of possibly damaging sites (CADD > 20), when compared to the ancient. However, a marked increase occurs in possibly damaging sites when the modern individuals are masked for European ancestry.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
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8. Figure 7 Novel Potentially Functional Variants
Novel variants are defined as variants not found in populations represented in the 1000 Genomes Project phase 3 release.36
(A) The modern group exhibits reduced levels of novel nonsynonymous alleles with respect to the ancient.
(B) The novel nonsynonymous variants are measured via CADD prediction scores of possibly damaging sites, where scores greater than 30 reflect potential deleterious changes that rank above the top 0.1% (red line). The ancient individuals show a larger distribution of potentially damaging alleles when compared to the modern.
The American Journal of Human Genetics  , DOI: ( /j.ajhg )
Copyright © 2018 American Society of Human Genetics Terms and Conditions