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Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

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Science  06 Apr 2018:
Vol. 360, Issue 6384, pp. 111-114
DOI: 10.1126/science.aao3297
  • Fig. 1 Sample location and corral enclosure at Botai.

    (A) Archaeological sites. The age (years ago) of the genomes considered is reported to the right of each site name. The number of genomes sequenced per site is reported between parentheses if greater than one. Triangles refer to the ancient genomes characterized here, whereas diamonds indicate those previously published. Blue refers to wild ancient individuals, light and dark green to the first domestic clade (Botai and Borly4), and yellow to individuals of the second domestic clade (DOM2). The Botai culture site of Krasnyi Yar is indicated with an asterisk, although no samples were analyzed from this site. (B) Magnetic gradient survey and excavation at Botai, with interpretation. The enclosure and its excavated boundary are indicated by red and yellow squares, respectively. Round black circles correspond to pit houses.

  • Fig. 2 Horse genetic affinities.

    (A) PCA of the genome variation present in 88 ancient- and modern-horse genomes. Only the first two principal components (PCA1 and PCA2) are shown. (B) Phylogenetic relationships. The tree was reconstructed on the basis of pairwise distances calculated with ~14.1 million transversion sites. Node supports derive from 100 bootstrap pseudoreplicates. The archaeological site and age (years ago) of ancient specimens are indicated in the first and last fields of the sample name. (C) Outgroup f3-statistics showing the pairwise genetic affinities.

  • Fig. 3 Admixture graphs.

    (A to F) The six scenarios tested. The scenario in panel (A) received decisive Bayes factor support, as indicated below each corresponding alternative scenario tested. Domestic-Ancient and Domestic-A or -B refer to three phylogenetic clusters identified within DOM2 (excluding Duk2): ancient individuals; modern Mongolian, Yakutian (including Tumeski_CGG101397), and Jeju horses; and all remaining modern breeds. (G) Posterior distributions of admixture proportions. p1 and p2 represent admixture proportions along the dotted branches in the best-supported scenario.

  • Fig. 4 Phenotypic and genomic changes associated with ferality.

    (A) Indices of the robustness of the third metacarpal bone in various horse populations. Bd, breadth at the middle of the diaphysis; GL, maximal or greatest length. Kent and Kumkeshu-Kozhai represent populations of Kazakhstan from the Iron Age and Eneolithic (Tersek culture), respectively. (B) Genotyping information at the TRPM1 locus (chr1, chromosome 1) and the PATN1 modifier (chr3, chromosome 3) for Botai-Borly4 horses. The absence, heterozygosis, and homozygosis of alleles strongly associated with leopard spotting are depicted in white, dark gray, and red, respectively. Crosses indicate insufficient data. The causative long tandem repeat (LTR) insertion at the TRPM1 locus is indicated by the number of reads overlapping both flanks of the insertion site. (C) Individual-based genetic loads. The purple circle shows the PH specimen from the 19th century.

  • Ancient genomes revisit the ancestry of domestic and Przewalski's horses

    Charleen Gaunitz, Antoine Fages, Kristian Hanghøj, Anders Albrechtsen, Naveed Khan, Mikkel Schubert, Andaine Seguin-Orlando, Ivy J. Owens, Sabine Felkel, Olivier Bignon-Lau, Peter de Barros Damgaard, Alissa Mittnik, Azadeh F. Mohaseb, Hossein Davoudi, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Eric Crubézy, Norbert Benecke, Sandra Olsen, Dorcas Brown, David Anthony, Ken Massy, Vladimir Pitulko, Aleksei Kasparov, Gottfried Brem, Michael Hofreiter, Gulmira Mukhtarova, Nurbol Baimukhanov, Lembi Lõugas, Vedat Onar, Philipp W. Stockhammer, Johannes Krause, Bazartseren Boldgiv, Sainbileg Undrakhbold, Diimaajav Erdenebaatar, Sébastien Lepetz, Marjan Mashkour, Arne Ludwig,Barbara Wallner, Victor Merz, Ilja Merz, Viktor Zaibert, Eske Willerslev, Pablo Librado, Alan K. Outram, Ludovic Orlando

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

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    • Materials and Methods
    • Figs. S1 to S34
    • Tables S1 to S7
    • Captions for Tables S8 to S18
    • References
    Table S8
    Ancient comparative panel. ID, temporal and cultural background associated with each of the 18 previously published ancient individuals included in this study, as well as inferred sex, accession number and study of publication, nuclear and mitochondrial coverages prior and after trimming and rescaling.
    Table S9
    Comparative panel of modern domestic horses. ID, breed, sex, accession number and study of publication, nuclear and mitochondrial coverages associated with each of the 28 modern horses included in this study.
    Table S10
    Raw morphological measurements of 375 horse specimens, for the third metacarpal. Measurement #1: Greatest length, #2: Lateral length, #3: Breadth at midshaft, #4: Depth at midshaft, #5: Proximal breadth, #6: Proximal articular depth, #7: Diameter of articular facet for Os carpale III, #8: Diameter of anterior facet for Os carpale IV, #8' Diameter of posterior facet for Os carpale IV, #9: Diameter of facet for Os carpal II, #10: Distal supra-articular breadth, #11: Distal articular breadth, #12: Depth of sagittal keel, #13: Smallest depth of medial condyle, #14: Greatest depth of medial condyle.
    Table S11
    Laboratory Procedures carried out on each sample sequenced in this study. (A) Summary information on DNA extractions, library construction, and amplification. (B) Independent libraries built with list of external index primers and internal indexed adapters selected as well as sequencing platform.
    Table S12
    Sequencing statistics per library for each sample sequenced in this study. nuDNA and mtDNA refer to nuclear DNA and mitochondrial DNA, respectively. All values have been calculated based on sequencing output prior to rescaling.
    Table S13
    Error rates for each substitution type. Reads showing mapping quality scores strictly inferior to 30 were disregarded. Bases showing quality scores strictly inferior to 20 were disregarded.
    Table S14
    Error rates for each substitution type. Reads showing mapping quality scores strictly inferior to 30 were disregarded. Bases showing quality scores strictly inferior to 30 were disregarded.
    Table S15
    Panel of modern and ancient horses included in mitochondrial analyses. Sample name, population, age, accession or registration number and reference associated with each individual.
    Table S16
    Statistical p-values for the test of direct ancestry. Shaded cells highlight significance, where the horse in the row belonged to a population that was directly ancestral to the population of the horse in the column
    Table S17
    WebGestalt analysis for genes overlapping significant LSDnorm regions. The 'branch' column indicates the population investigated, as labeled in Fig. S34. Branch 8, for example, corresponds to the branch ancestral to Przewalski's horses. Only categories with an adjusted pvalue < 0.1 are shown.
    Table S18
    Developmental stages and anatomical body parts where genes overlapping significant LSDnorm windows are transcribed, as revealed by Bgee (173). The 'branch' column indicates the population investigated, as labeled in Fig. S34. Branch 4, for example, corresponds to the branch ancestral to Botai and Borly4 horses. No over-represented categories were found in lineages 8 and 9. Only transcriptional categories with an adjusted p-value < 0.1 are shown.

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