van Vuure, C. & van Vuure, T. Retracing the Aurochs: History, Morphology and Ecology of an Extinct Wild Ox (Pensoft Publishers, 2005).
de Carvalho, C. N. et al. Aurochs roamed along the SW coast of Andalusia (Spain) during Late Pleistocene. Sci. Rep. 12, 9911 (2022).
Wang, X., Flynn, L. J. & Fortelius, M. Fossil Mammals of Asia: Neogene Biostratigraphy and Chronology (Columbia Univ. Press, 2013).
Schulz, E. & KaiSer, T. M. Feeding strategy of the Urus Bos primigenius BOJANUS, 1827 from the Holocene of Denmark. Cour. Forsch. Inst. Senckenberg 259, 155â164 (2007).
Bro-Jørgensen, M. H. et al. Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. J. Archaeol. Sci. 99, 47â54 (2018).
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506â6511 (2018).
Bailey, J. F. et al. Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species. Proc. Biol. Sci. 263, 1467â1473 (1996).
Troy, C. S. et al. Genetic evidence for Near-Eastern origins of European cattle. Nature 410, 1088â1091 (2001).
Park, S. D. E. et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 16, 234 (2015).
Verdugo, M. P. et al. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 365, 173â176 (2019).
Ginja, C. et al. Iron age genomic data from Althiburos â Tunisia renew the debate on the origins of African taurine cattle. iScience 26, 107196 (2023).
Svendsen, J. I. et al. Late Quaternary ice sheet history of northern Eurasia. Quat. Sci. Rev. 23, 1229â1271 (2004).
Wright, E. in Cattle and People: Interdisciplinary Approaches to an Ancient Relationship (eds Wright, E. & Ginja, C.) 3â27 (Lockwood Press, 2022).
Hewitt, G. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. Lond. 68, 87â112 (1999).
Linseele, V. Size and size change of the African aurochs during the Pleistocene and Holocene. J. Afr. Archaeol. 2, 165â185 (2004).
Lefèvre, D., Raynal, J.-P., Vernet, G., Kieffer, G. & Piperno, M. Tephro-stratigraphy and the age of ancient Southern Italian Acheulean settlements: the sites of Loreto and Notarchirico (Venosa, Basilicata, Italy). Quat. Int. 223â224, 360â368 (2010).
Pereira, A. et al. The earliest securely dated hominin fossil in Italy and evidence of Acheulian occupation during glacial MIS 16 at Notarchirico (Venosa, Basilicata, Italy). J. Quat. Sci. 30, 639â650 (2015).
Cassoli, P. F., Di Stefano, G. & A., T. in Notarchirico: Un Sito del Pleistocene Medio Iniziale nel Bacino (ed. di Piperno, M.) 361â438 (Osanna, 1999).
Lambeck, K., Esat, T. M. & Potter, E.-K. Links between climate and sea levels for the past three million years. Nature 419, 199â206 (2002).
Batchelor, C. L. et al. The configuration of Northern Hemisphere ice sheets through the Quaternary. Nat. Commun. 10, 3713 (2019).
Otvos, E. G. The Last Interglacial Stage: definitions and marine highstand, North America and Eurasia. Quat. Int. 383, 158â173 (2015).
Leonardi, M., Boschin, F., Boscato, P. & Manica, A. Following the niche: the differential impact of the last glacial maximum on four European ungulates. Commun. Biol. 5, 1038 (2022).
Helmens, K. F. The Last InterglacialâGlacial cycle (MIS 5â2) re-examined based on long proxy records from central and northern Europe. Quat. Sci. Rev. 86, 115â143 (2014).
Kosintsev, P. A. & Bachura, O. P. Late Pleistocene and Holocene mammal fauna of the Southern Urals. Quat. Int. 284, 161â170 (2013).
Robin, M. et al. Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex. Mol. Ecol. 31, 3548â3565 (2022).
Miller, W. et al. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl Acad. Sci. USA 109, E2382âE2390 (2012).
Lord, E. et al. Population dynamics and demographic history of Eurasian collared lemmings. BMC Ecol. Evol. 22, 126 (2022).
Murray, C., Huerta-Sanchez, E., Casey, F. & Bradley, D. G. Cattle demographic history modelled from autosomal sequence variation. Phil. Trans. R. Soc. B 365, 2531â2539 (2010).
Sinding, M.-H. S. et al. Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 24, 103226 (2021).
Bergman, J. et al. Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nat. Commun. 14, 7679 (2023).
Erven, J. A. M. et al. A high-coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation. Mol. Biol. Evol. 41, msae076 (2024).
MacLeod, I. M., Larkin, D. M., Lewin, H. A., Hayes, B. J. & Goddard, M. E. Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Mol. Biol. Evol. 30, 2209â2223 (2013).
Clutton-Brock, T. Mammal Societies (Wiley, 2016).
Cubric-Curik, V. et al. Largeâscale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol. Appl. 15, 663â678 (2022).
Makarewicz, C. & Tuross, N. Finding fodder and tracking transhumance: isotopic detection of goat domestication processes in the Near East. Curr. Anthropol. 53, 495â505 (2012).
Bollongino, R. et al. Modern taurine cattle descended from small number of near-eastern founders. Mol. Biol. Evol. 29, 2101â2104 (2012).
Scheu, A. et al. The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genet. 16, 54 (2015).
Upadhyay, M. R. et al. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity 118, 169â176 (2017).
Marshall, F. B., Dobney, K., Denham, T. & Capriles, J. M. Evaluating the roles of directed breeding and gene flow in animal domestication. Proc. Natl Acad. Sci. USA 111, 6153â6158 (2014).
Götherström, A. et al. Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proc. Biol. Sci. 272, 2345â2350 (2005).
Achilli, A. et al. The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One 4, e5753 (2009).
Yang, D. Y., Eng, B., Waye, J. S., Dudar, J. C. & Saunders, S. R.Improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539â543 (1998).
Mattiangeli, V., Cassidy, L. M., Daly, K. G., Mullin, V. E. & Verdugo, M. Multi-step ancient DNA extraction protocol for bone and teeth. Protocols.io https://doi.org/10.17504/protocols.io.6qpvr45b2gmk/v1 (2023).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758â15763 (2013).
Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742â751 (2017).
Mattiangeli, V., Cassidy, L. M., Daly, K. G. & Mullin, V. E. Bleach extraction protocol: damaged or degraded DNA recovery from bone or tooth powder. Protocols.io https://doi.org/10.17504/protocols.io.8epv5j88nl1b/v1 (2023).
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010).
Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014).
Botigué, L. R. et al. Ancient European dog genomes reveal continuity since the Early Neolithic. Nat. Commun. 8, 16082 (2017).
Carøe, C. et al. Singleâtube library preparation for degraded DNA. Methods Ecol. Evol. 9, 410â419 (2018).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10â12 (2011).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
Li, H. & Durbin, R. Fast and accurate short read alignment with BurrowsâWheeler transform. Bioinformatics 25, 1754â1760 (2009).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078â2079 (2009).
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682â1684 (2013).
Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229â2234 (2014).
Okonechnikov, K., Conesa, A. & GarcÃa-Alcalde, F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32, 292â294 (2016).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114â2120 (2014).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv https://doi.org/10.48550/arXiv.1303.3997 (2013).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156â2158 (2011).
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15, 356 (2014).
Hahn, C., Bachmann, L. & Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing readsâa baiting and iterative mapping approach. Nucleic Acids Res. 41, e129 (2013).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24â26 (2011).
Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792â1797 (2004).
Gouy, M., Tannier, E., Comte, N. & Parsons, D. P. Seaview Version 5: a multiplatform software for multiple sequence alignment, molecular phylogenetic analyses, and tree reconciliation. Methods Mol. Biol. 2231, 241â260 (2021).
Bouckaert, R. R. & Drummond, A. J. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol. Biol. 17, 42 (2017).
Drummond, A. J., Rambaut, A., Shapiro, B. & Pybus, O. G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22, 1185â1192 (2005).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901â904 (2018).
Chang, T.-C., Yang, Y., Retzel, E. F. & Liu, W.-S. Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development. Proc. Natl Acad. Sci. USA 110, 12373â12378 (2013).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307â321 (2010).
Browning, B. L., Tian, X., Zhou, Y. & Browning, S. R. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880â1890 (2021).
Browning, B. L., Zhou, Y. & Browning, S. R. A one-penny imputed genome from next-generation reference panels. Am. J. Hum. Genet. 103, 338â348 (2018).
Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120â126 (2021).
Schiffels, S. & Wang, K. MSMC and MSMC2: the Multiple Sequentially Markovian Coalescent. Methods Mol. Biol. 2090, 147â166 (2020).
Chen, N. et al. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat. Commun. 9, 2337 (2018).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559â575 (2007).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526â528 (2019).
Meisner, J. & Albrechtsen, A. Inferring population structure and admixture proportions in low-depth NGS data. Genetics 210, 719â731 (2018).
Soraggi, S., Wiuf, C. & Albrechtsen, A. Powerful inference with the D-statistic on low-coverage whole-genome data. G3 8, 551â566 (2018).
Maier, R. et al. On the limits of fitting complex models of population history to f-statistics. eLife 12, e85492 (2023).
Skotte, L., Korneliussen, T. S. & Albrechtsen, A. Estimating individual admixture proportions from next generation sequencing data. Genetics 195, 693â702 (2013).
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A. & Mayrose, I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179â1191 (2015).
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611â2620 (2005).
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
Harney, Ã., Patterson, N., Reich, D. & Wakeley, J. Assessing the performance of qpAdm: a statistical tool for studying population admixture. Genetics 217, iyaa045 (2021).
Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207â211 (2015).
Lisiecki, L. E. & Raymo, M. E. A PlioceneâPleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanogr. Paleoclimatol. 20, PA1003 (2005).