The evolutionary history of dogs in the Americas

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Science  06 Jul 2018:
Vol. 361, Issue 6397, pp. 81-85
DOI: 10.1126/science.aao4776
  • Fig. 1 Sample locations and ancestry of PCDs.

    (A) A map depicting the locations and ages of the archaeological remains analyzed in this study. Each dot represents a single sample, and multiple samples per archaeological site are grouped in boxes. Sites mentioned in the text are labeled. BP, before the present. (B) A tip-calibrated Bayesian mitochondrial phylogenetic tree of dogs within haplogroup A. This analysis was conducted with 66 novel ancient mitogenomes (all genomes with at least 10× coverage) together with 145 publicly available mitogenomes from both modern and ancient canids (3) (fig. S6). Red branches represent modern dogs, dark blue represents PCDs, and light blue denotes ancient DNA from Arctic dogs. Blue bars on nodes represent 95% HPD ages. The gray shaded area represents the time frame during which people likely entered the Americas based on the age of divergence between Native Americans and ancient Beringians (~20,000 years ago) (12) and the flooding of the Bering land bridge (~11,000 years ago) (11). (C) A neighbor-joining tree built with whole genomes (3). (D) An admixture graph constructed with Treemix (on the basis of transversions) (3, 18) depicting the relationship between PCDs [including the Port au Choix (AL3194) and Weyanoke Old Town (AL3223) samples] and other dog, wolf, and CTVT populations. The scale bar shows 10 times the average standard error (s.e.) of the entries in the sample covariance matrix (18).

  • Fig. 2 Legacy of PCDs in modern American dogs.

    (A) A map showing the locations of dog populations obtained from (9) and their degrees of relatedness (D statistics) to the ~4000-year-old Port au Choix dog (AL3194) [see (3) and fig. S14]. Higher values (in red) represent closer relatedness. The location of the founder CTVT individual, labeled in the plot, is unknown. (B) A map depicting the multiple introductions of dogs into the Americas.

Supplementary Materials

  • The evolutionary history of dogs in the Americas

    Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen, Aleksei K. Kasparov, Young-Mi Kwon, Pavel A. Nikolskiy, Carlos Peraza Lope, Aurélie Manin, Terrance Martin, Michael Meyer, Kelsey Noack Myers, Mark Omura, Jean-Marie Rouillard, Elena Y. Pavlova, Paul Sciulli, Mikkel-Holger S. Sinding, Andrea Strakova, Varvara V. Ivanova, Christopher Widga, Eske Willerslev, Vladimir V. Pitulko, Ian Barnes, M. Thomas P. Gilbert, Keith M. Dobney, Ripan S. Malhi, Elizabeth P. Murchison, Greger Larson, Laurent A. F. Frantz

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S27
    • Tables S3 to S8 and S12 to S16
    • Captions for Tables S1, S2, and S9 to S11
    • References
    Table S1
    Information about samples ancient samples sequenced in this study including provenance, age (radiocarbon or stratigraphic information), and sequencing statistics (endogeneous content etc.). N_SNP_call corresponds to the number of sites from our ~6M sites that were call in each sample. Analysed Nuclear and mtDNA Analysed columns corresponds to sample that were (1) and were not (0) analysed for nuclear and mtDNA analyses respectively. mtDNA capture column indicates whether mtDNA was enriched using target capture (0, no; 1, yes).
    Table S2
    Table containing information (coverage, accession etc.) of modern whole genomes used in this study.
    Table S9
    Sample code used as population name for SNP array analysis.
    Table S10
    Results of f4 ratio analysis depicted in Figure S18 (see Table S9 for population code).
    Table S11
    Results of f4 ratio analysis used to estimate proportion of PCD ancestry in Arctic breeds. This table include results for both SNP array and Genome-wide analyses.

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