Supplementary Materials

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

Download Supplement
  • 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.