CoChat
Sign Up
Cited by 285

The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Fages, Antoine, Hanghøj, Kristian, Khan, Naveed, Gaunitz, Charleen, Seguin-Orlando, Andaine, Leonardi, Michela, McCrory Constantz, Christian, Gamba, Cristina, Al-Rasheid, Khaled A.S., Albizuri, Silvia, Alfarhan, Ahmed H., Allentoft, Morten, Alquraishi, Saleh, Anthony, David, Baimukhanov, Nurbol, Barrett, James H., Bayarsaikhan, Jamsranjav, Benecke, Norbert, Bernáldez-Sánchez, Eloísa, Berrocal-Rangel, Luis, Biglari, Fereidoun, Boessenkool, Sanne, Boldgiv, Bazartseren, Brem, Gottfried, Brown, Dorcas, Burger, Joachim, Crubézy, Eric, Daugnora, Linas, Davoudi, Hossein, de Barros Damgaard, Peter, de los Ángeles de Chorro y de Villa-Ceballos, María, Deschler-Erb, Sabine, Detry, Cleia, Dill, Nadine, do Mar Oom, Maria, Dohr, Anna, Ellingvåg, Sturla, Erdenebaatar, Diimaajav, Fathi, Homa, Felkel, Sabine, Fernández-Rodríguez, Carlos, García-Viñas, Esteban, Germonpré, Mietje, Granado, José D., Hallsson, Jón H., Hemmer, Helmut, Hofreiter, Michael, Kasparov, Aleksei, Khasanov, Mutalib, Khazaeli, Roya, Kosintsev, Pavel, Kristiansen, Kristian, Kubatbek, Tabaldiev, Kuderna, Lukas, Kuznetsov, Pavel, Laleh, Haeedeh, Leonard, Jennifer A., Lhuillier, Johanna, Liesau von Lettow-Vorbeck, Corina, Logvin, Andrey, Lõugas, Lembi, Ludwig, Arne, Luis, Cristina, Arruda, Ana Margarida, Marques-Bonet, Tomas, Matoso Silva, Raquel, Merz, Victor, Mijiddorj, Enkhbayar, Miller, Bryan K., Monchalov, Oleg, Mohaseb, Fatemeh A., Morales, Arturo, Nieto-Espinet, Ariadna, Nistelberger, Heidi, Onar, Vedat, Pálsdóttir, Albína H., Pitulko, Vladimir, Pitskhelauri, Konstantin, Pruvost, Mélanie, Rajic Sikanjic, Petra, Rapan Papeša, Anita, Roslyakova, Natalia, Sardari, Alireza, Sauer, Eberhard, Schafberg, Renate, Scheu, Amelie, Schibler, Jörg, Schlumbaum, Angela, Serrand, Nathalie, Serres-Armero, Aitor, Shapiro, Beth, Sheikhi Seno, Shiva, Shevnina, Irina, Shidrang, Sonia, Southon, John, Star, Bastiaan, Sykes, Naomi, Taheri, Kamal, Taylor, William, Teegen, Wolf-Rüdiger, Trbojević Vukičević, Tajana, Trixl, Simon, Tumen, Dashzeveg, Undrakhbold, Sainbileg, Usmanova, Emma, Vahdati, Ali, Valenzuela-Lamas, Silvia, Viegas, Catarina, Wallner, Barbara, Weinstock, Jaco, Zaibert, Victor, Clavel, Benoit, Lepetz, Sébastien, Mashkour, Marjan, Helgason, Agnar, Stefánsson, Kári, Barrey, Eric, Willerslev, Eske, Outram, Alan K., Librado, Pablo, Orlando, Ludovic·2019·Cell
DOI 10.1016/j.cell.2019.03.049PMC PMC6547883
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cell.2019.03.049

Cites

12 of 12 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Large-scale population replacement occurred in dogs, wolves, horses, pigs and crops such as potato.

    “Large-scale population replacement occurred in dogs 278 , wolves 196,279,280 , horses 148,281 , pigs 282 and crops such as potato 283 .”

    From Ancient DNA analysis (2021) · cites this paper as [148]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 76

  1. Abad, 2011, Cantorella (Maldà, Urgell), un nou assentament a l’aire lliure del neolític final-calcolític i del bronze ple a la vall del Corb, Tribuna d'Arqueologia, 2011
  2. Arbuckle, 2012, Pastoralism, Provisioning, and Power at Bronze Age Acemhöyük, Turkey, Am. Anthropol., 114, 462, 10.1111/j.1548-1433.2012.01446.x · DOI
  3. Barlow, 2018, Consensify: a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates, bioRxiv
  4. Barrett, 2009, New Excavations at the Brough of Deerness: Power and Religion in Viking Age Scotland, J. North Atlantic, 81, 10.3721/037.002.0108 · DOI
  5. Benjamini, 1995, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, J. R. Stat. Soc. Series B Stat. Methodol., 57, 289, 10.1111/j.2517-6161.1995.tb02031.x · DOI · Paper page
  6. Bertašius, 2001, Viking age horse graves from Kaunas region (Middle Lithuania), Int. J. Osteoarchaeol., 11, 387, 10.1002/oa.580 · DOI
  7. Boeskorov, 2018, A study of a frozen mummy of a wild horse from the Holocene of Yakutia, East Siberia, Russia, Mammal Res., 63, 1, 10.1007/s13364-018-0362-4 · DOI
  8. Briggs, 2007, Patterns of damage in genomic DNA sequences from a Neandertal, Proc. Natl. Acad. Sci. USA, 104, 14616, 10.1073/pnas.0704665104 · DOI · Paper page
  9. Briggs, 2010, Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA, Nucleic Acids Res., 38, e87, 10.1093/nar/gkp1163 · DOI · Paper page
  10. Charlesworth, 2009, Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation, Nat. Rev. Genet., 10, 195, 10.1038/nrg2526 · DOI
  11. Corbin, 2010, Linkage disequilibrium and historical effective population size in the Thoroughbred horse, Anim. Genet., 41, 8, 10.1111/j.1365-2052.2010.02092.x · DOI
  12. Cruz, 2008, The legacy of domestication: accumulation of deleterious mutations in the dog genome, Mol. Biol. Evol., 25, 2331, 10.1093/molbev/msn177 · DOI · Paper page
  13. Der Sarkissian, 2015, Evolutionary genomics and conservation of the endangered Przewalski’s horse, Curr. Biol., 25, 2577, 10.1016/j.cub.2015.08.032 · DOI
  14. Durand, 2011, Testing for ancient admixture between closely related populations, Mol. Biol. Evol., 28, 2239, 10.1093/molbev/msr048 · DOI · Paper page
  15. Dyson, 1989, The Iron Age architecture at Hasanlu: an essay, Expedition, 31, 107
  16. Dyson, 1999, The Achaemenid painted pottery of Hasanlu IIIA, Anatolian Studies, 49, 101, 10.2307/3643065 · DOI
  17. Einarsson, 1995, The Settlement of Iceland, A Critical Approach: Granastaðair and the Ecological Heritage, Reykjavík: Hið íslenzka bókmentafélag
  18. Felkel, 2018, Asian horses deepen the MSY phylogeny, Anim. Genet., 49, 90, 10.1111/age.12635 · DOI
  19. Gamba, 2016, Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing, Mol. Ecol. Resour., 16, 459, 10.1111/1755-0998.12470 · DOI
  20. Gaunitz, 2018, Ancient genomes revisit the ancestry of domestic and Przewalski’s horses, Science, 360, 111, 10.1126/science.aao3297 · DOI · Paper page
  21. Green, 2010, A draft sequence of the Neandertal genome, Science, 328, 710, 10.1126/science.1188021 · DOI · Paper page
  22. Hall, 2016, Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data, Animal, 10, 1778, 10.1017/S1751731116000914 · DOI
  23. Haller, 2017, SLiM 2: Flexible, Interactive Forward Genetic Simulations, Mol. Biol. Evol., 34, 230, 10.1093/molbev/msw211 · DOI
  24. Hansman, 1970, A Sasanian Repository at Shahr-I Qūmis, JRAS, 102, 142
  25. Hansman, 1970, Excavations at Shahr-I Qūmis, The Journal of Royal Asiatic Society of Great Britain and Ireland, 1, 29, 10.1017/S0035869X00127972 · DOI
  26. Hill, 2010, Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance, Anim. Genet., 41, 56, 10.1111/j.1365-2052.2010.02104.x · DOI
  27. Jónsson, 2014, Speciation with gene flow in equids despite extensive chromosomal plasticity, Proc. Natl. Acad. Sci. USA, 111, 18655, 10.1073/pnas.1412627111 · DOI
  28. Kamm, 2018, Efficiently inferring the demographic history of many populations with allele count data, bioRxiv
  29. Keane, 2006, Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified, BMC Evol. Biol., 6, 29, 10.1186/1471-2148-6-29 · DOI
  30. Kosintsev, 2013, Comment on “The Earliest Horse Harnessing and Milking.”, Tyragetia, 7, 405
  31. Kousathanas, 2013, A comparison of models to infer the distribution of fitness effects of new mutations, Genetics, 193, 1197, 10.1534/genetics.112.148023 · DOI
  32. Kovalev, 2016, A ritual complex with deer stones at Uushigiin Uvur, Mongolia: composition and construction stages, Archaeol. Ethnol. Anthropol. Eurasia, 44, 82, 10.17746/1563-0110.2016.44.1.082-092 · DOI
  33. Kristjansson, 2014, The effect of the ‘Gait keeper’ mutation in the DMRT3 gene on gaiting ability in Icelandic horses, J. Anim. Breed. Genet., 131, 415, 10.1111/jbg.12112 · DOI
  34. Lefort, 2015, FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program, Mol. Biol. Evol., 32, 2798, 10.1093/molbev/msv150 · DOI
  35. Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 · DOI · Paper page
  36. Librado, 2015, Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments, Proc. Natl. Acad. Sci. USA, 112, E6889, 10.1073/pnas.1513696112 · DOI
  37. Librado, 2017, Ancient genomic changes associated with domestication of the horse, Science, 356, 442, 10.1126/science.aam5298 · DOI
  38. Liesau, 2005, Arqueozoología del caballo en la antigua Iberia, Gladius, 25, 187, 10.3989/gladius.2005.28 · DOI
  39. Lindgren, 2004, Limited number of patrilines in horse domestication, Nat. Genet., 36, 335, 10.1038/ng1326 · DOI
  40. Lippold, 2011, Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication, BMC Evol. Biol., 11, 328, 10.1186/1471-2148-11-328 · DOI
  41. Lira, 2010, Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses, Mol. Ecol., 19, 64, 10.1111/j.1365-294X.2009.04430.x · DOI
  42. Marciniak, 2017, Harnessing ancient genomes to study the history of human adaptation, Nat. Rev. Genet., 18, 659, 10.1038/nrg.2017.65 · DOI
  43. Martin, 2015, Evaluating the use of ABBA-BABA statistics to locate introgressed loci, Mol. Biol. Evol., 32, 244, 10.1093/molbev/msu269 · DOI
  44. McCue, 2008, Glycogen synthase (GYS1) mutation causes a novel skeletal muscle glycogenosis, Genomics, 91, 458, 10.1016/j.ygeno.2008.01.011 · DOI
  45. McDonald, 1991, Adaptive protein evolution at the Adh locus in Drosophila, Nature, 351, 652, 10.1038/351652a0 · DOI
  46. McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 · DOI · Paper page
  47. Meyer, 2010, Illumina sequencing library preparation for highly multiplexed target capture and sequencing, Cold Spring Harb. Protoc., 2010, 10.1101/pdb.prot5448 · DOI
  48. Miller, 2006, A Xiongnu tomb complex: Excavations at Gol Mod 2 Cemetery, Mongolia (2002–2005), Mongolian J. Anthropol. Arc. Ethnol., 2, 1
  49. Negahbān, 1974, Sagzabad Excavation Report. Iran, 12, 216
  50. Nieto Espinet, 2016, Seguint les traces de la transhumància. Aproximació teòrica a partir dels resultats arqueozoològics de la fortalesa dels Vilars (Arbeca, Garrigues), Revista D’arqueologia de Ponent, 26, 11, 10.21001/rap.2016.26.1 · DOI
  51. Olalde, 2018, The Beaker phenomenon and the genomic transformation of northwest Europe, Nature, 555, 190, 10.1038/nature25738 · DOI · Paper page
  52. Onar, 2013, Animal skeletal remains of the Theodosius harbor: general overview, Turk. J. Vet. Anim. Sci., 37, 81
  53. Orlando, 2013, Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse, Nature, 499, 74, 10.1038/nature12323 · DOI · Paper page
  54. Outram, 2009, The earliest horse harnessing and milking, Science, 323, 1332, 10.1126/science.1168594 · DOI
  55. Paradis, 2004, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, 20, 289, 10.1093/bioinformatics/btg412 · DOI · Paper page
  56. Pearson, 2005, Modulating Hox gene functions during animal body patterning, Nat. Rev. Genet., 6, 893, 10.1038/nrg1726 · DOI · Paper page
  57. Pedersen, 2017, The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit, Genetics, 205, 787, 10.1534/genetics.116.193821 · DOI
  58. Pollard, 2010, Detection of nonneutral substitution rates on mammalian phylogenies, Genome Res., 20, 110, 10.1101/gr.097857.109 · DOI · Paper page
  59. Ramsey, 2009, Bayesian Analysis of Radiocarbon Dates, Radiocarbon, 51, 337, 10.1017/S0033822200033865 · DOI · Paper page
  60. Schubert, 2014, Prehistoric genomes reveal the genetic foundation and cost of horse domestication, Proc. Natl. Acad. Sci. USA, 111, E5661, 10.1073/pnas.1416991111 · DOI · Paper page
  61. Schubert, 2014, Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX, Nat. Protoc., 9, 1056, 10.1038/nprot.2014.063 · DOI · Paper page
  62. Schubert, 2016, AdapterRemoval v2: rapid adapter trimming, identification, and read merging, BMC Res. Notes, 9, 88, 10.1186/s13104-016-1900-2 · DOI
  63. Schubert, 2017, Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages, J. Archaeol. Sci., 72, 147, 10.1016/j.jas.2016.12.005 · DOI · Paper page
  64. Sheikhi Seno, 2012, Subsistence Economy of the Lapui settlement of Tepe Mehr Ali Fars on the basis of the archaeozoological analysis, J. Iran. Archaeol., 2, 39
  65. Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 · DOI · Paper page
  66. Uerpmann, 1990, Die Domestikation des Pferdes im Chalkolihikum West-und Mitteleuropas, mit 10 Textabbildungen, Madrider Mitteilungen, 31, 109
  67. Vieira, 2016, Improving the estimation of genetic distances from Next-Generation Sequencing data, Biol. J. Linn. Soc. Lond., 117, 139, 10.1111/bij.12511 · DOI
  68. Vukičević, 2017, Contribution to understanding Avar burials with equids in Croatia: detailed archaeozoological analysis, Rev. Med. Vet. (Toulouse), 168, 73
  69. Wallner, 2017, Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions, Curr. Biol., 27, 2029, 10.1016/j.cub.2017.05.086 · DOI
  70. Wang, 2017, WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit, Nucleic Acids Res., 45, W130, 10.1093/nar/gkx356 · DOI
  71. Warmuth, 2011, European domestic horses originated in two holocene refugia, PLoS ONE, 6, e18194, 10.1371/journal.pone.0018194 · DOI
  72. Williamson, 2014, Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora, PLoS Genet., 10, e1004622, 10.1371/journal.pgen.1004622 · DOI
  73. Wilson Sayres, 2014, Natural selection reduced diversity on human y chromosomes, PLoS Genet., 10, e1004064, 10.1371/journal.pgen.1004064 · DOI
  74. Wutke, 2018, Decline of genetic diversity in ancient domestic stallions in Europe, Sci. Adv., 4, eaap9691, 10.1126/sciadv.aap9691 · DOI
  75. Xu, 1994, The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region, Gene, 148, 357, 10.1016/0378-1119(94)90713-7 · DOI
  76. Youn, 2007, Dating the Tavan Tolgoi Site, Mongolia: Burials of the Nobility from Genghis Khan’s Era, Radiocarbon, 49, 685, 10.1017/S0033822200042570 · DOI

Cited by

Sorted by citations

Metadata

Authors
Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin-Orlando, A., Leonardi, M., McCrory Constantz, C., Gamba, C., Al-Rasheid, K. A. S., Albizuri, S., Alfarhan, A. H., Allentoft, M., Alquraishi, S., Anthony, D., Baimukhanov, N., Barrett, J. H., Bayarsaikhan, J., Benecke, N., Bernáldez-Sánchez, E., Berrocal-Rangel, L., Biglari, F., Boessenkool, S., Boldgiv, B., Brem, G., Brown, D., Burger, J., Crubézy, E., Daugnora, L., Davoudi, H., de Barros Damgaard, P., de los Ángeles de Chorro y de Villa-Ceballos, M., Deschler-Erb, S., Detry, C., Dill, N., do Mar Oom, M., Dohr, A., Ellingvåg, S., Erdenebaatar, D., Fathi, H., Felkel, S., Fernández-Rodríguez, C., García-Viñas, E., Germonpré, M., Granado, J. D., Hallsson, J. H., Hemmer, H., Hofreiter, M., Kasparov, A., Khasanov, M., Khazaeli, R., Kosintsev, P., Kristiansen, K., Kubatbek, T., Kuderna, L., Kuznetsov, P., Laleh, H., Leonard, J. A., Lhuillier, J., Liesau von Lettow-Vorbeck, C., Logvin, A., Lõugas, L., Ludwig, A., Luis, C., Arruda, A. M., Marques-Bonet, T., Matoso Silva, R., Merz, V., Mijiddorj, E., Miller, B. K., Monchalov, O., Mohaseb, F. A., Morales, A., Nieto-Espinet, A., Nistelberger, H., Onar, V., Pálsdóttir, A. H., Pitulko, V., Pitskhelauri, K., Pruvost, M., Rajic Sikanjic, P., Rapan Papeša, A., Roslyakova, N., Sardari, A., Sauer, E., Schafberg, R., Scheu, A., Schibler, J., Schlumbaum, A., Serrand, N., Serres-Armero, A., Shapiro, B., Sheikhi Seno, S., Shevnina, I., Shidrang, S., Southon, J., Star, B., Sykes, N., Taheri, K., Taylor, W., Teegen, W.-R., Trbojević Vukičević, T., Trixl, S., Tumen, D., Undrakhbold, S., Usmanova, E., Vahdati, A., Valenzuela-Lamas, S., Viegas, C., Wallner, B., Weinstock, J., Zaibert, V., Clavel, B., Lepetz, S., Mashkour, M., Helgason, A., Stefánsson, K., Barrey, E., Willerslev, E., Outram, A. K., Librado, P., & Orlando, L.
Venue
Cell
Publisher
Elsevier BV
Published
2019-05
Volume
177
Issue
6
Pages
1419-1435.e31
ISSN
0092-8674
DOI
10.1016/j.cell.2019.03.049
PMC
PMC6547883
Cited by
285
References
12
Language
en
Licence
Funders
  • Russian Science Foundation (18-18-00137, 16-18-10265)
  • Asia Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CR13I1_140638, ANS-1417036)
  • Horizon 2020 Framework Programme
  • Marie Curie
  • Eesti Teadusagentuur
  • National Science Foundation
  • Generalitat de Catalunya
  • European Research Council (681605)
  • European Regional Development Fund (U01 MH106874)
  • Université de Toulouse
  • Estonian Research Competency Council (PRG29)
  • Villum Fonden
  • H2020 Marie Skłodowska-Curie Actions (MSCA-IF-67852)
  • Norges Forskningsråd (230821/F20)
  • Ministerio de Economía y Competitividad (BFU2017-86471-P, HAR2016-77600-P)
  • Howard Hughes Medical Institute
  • “la Caixa” Foundation
  • Danmarks Grundforskningsfond (DNRF94)
  • European Commission
  • Deanship of Scientific Research, King Saud University
  • Ministry of Education and Science of the Russian Federation (2017/\u03A04, 33.1907)
  • Fundação para a Ciência e a Tecnologia (SFRH/BPD/100511/2014)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review