FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
iScience2023; 26(3); 106144; doi: 10.1016/j.isci.2023.106144

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

Abstract: Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
© 2023 The Author(s).
Get Full Text
Publication Date: 2023-02-05 PubMed ID: 36843848PubMed Central: PMC9950528DOI: 10.1016/j.isci.2023.106144Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research paper explores using DNA methylation profiles to accurately determine the age-at-death for ancient horses and detecting if they were castrated. The study demonstrates the potential to learn more about past animal husbandry and rituals and could eventually be adapted to human remains for understanding age mortality profiles in ancient societies.

Introduction and research approach

  • The authors start by discussing the challenges of profiling the age of archaeological bone assemblages due to the fragmented nature of the fossils and the absence of universal skeletal markers. DNA methylation clocks, which track age-related changes in an organism’s DNA, are suggested as an alternative tool for estimating age-at-death.
  • For this research, the team used a DNA methylation clock based on 31,836 markers known as CpG sites. They also used dental age markers in horses to verify the age predictions.
  • The study examined 84 ancient horse remains to test the efficacy of this method.

Development of a cost-effective method

  • The authors developed a capture assay to analyze the horse remains. A capture assay is a molecular biology method used to isolate and examine specific DNA sequences.
  • They demonstrated that this approach could provide reliable age estimates at a much lower cost than whole-genome sequencing, the more traditional method for genetic analysis.

Evaluating castration practices

  • In addition to estimating age-at-death, the researchers also used DNA methylation patterns to assess whether the ancient horses had been castrated. Castration practices can give insights into breeding strategies, work duties, and ritual practices in ancient societies.

Implications and potential applications

  • The authors argue that through obtaining accurate age-at-death profiles and knowledge about castration practices, we can gain deeper insights into past husbandry and ritual practices involving horses.
  • Last but not least, they propose that their method, once extended to human remains, holds the potential to reveal age mortality profiles in ancient societies, contributing to our understanding of past demographics and mortality risks.

Cite This Article

APA
Liu X, Seguin-Orlando A, Chauvey L, Tressières G, Schiavinato S, Tonasso-Calvière L, Aury JM, Perdereau A, Wagner S, Clavel P, Estrada O, Pan J, Ma Y, Enk J, Devault A, Klunk J, Lepetz S, Clavel B, Jiang L, Wincker P, Collin YRH, Sarkissian C, Orlando L. (2023). DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience, 26(3), 106144. https://doi.org/10.1016/j.isci.2023.106144

Publication

iScience
ISSN: 2589-0042
NlmUniqueID: 101724038
Country: United States
Language: English
Volume: 26
Issue: 3
Pages: 106144
PII: 106144

Researcher Affiliations

Liu, Xuexue
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Seguin-Orlando, Andaine
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Chauvey, Lorelei
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Tressières, Gaëtan
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Schiavinato, Stéphanie
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Tonasso-Calvière, Laure
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Aury, Jean-Marc
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Évry, Université Paris-Saclay, 91042 Évry, France.
Perdereau, Aude
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Évry, Université Paris-Saclay, 91042 Évry, France.
Wagner, Stefanie
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
  • INRAE Division Ecology and Biodiversity (ECODIV), Castanet Tolosan, France.
Clavel, Pierre
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Estrada, Oscar
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Pan, Jianfei
  • Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China.
Ma, Yuehui
  • Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China.
Enk, Jacob
  • Daicel Arbor Biosicences, Ann Arbor, MI, USA.
Devault, Alison
  • Daicel Arbor Biosicences, Ann Arbor, MI, USA.
Klunk, Jennifer
  • Daicel Arbor Biosicences, Ann Arbor, MI, USA.
Lepetz, Sébastien
  • Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 Rue Buffon, 75005 Paris, France.
Clavel, Benoit
  • Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 Rue Buffon, 75005 Paris, France.
Jiang, Lin
  • Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China.
Wincker, Patrick
  • Genoscope, Institut de biologie François Jacob, CEA, Université d'Évry, Université Paris-Saclay, 91042 Évry, France.
Collin, Yvette Running Horse
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Sarkissian, Clio Der
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France.

Conflict of Interest Statement

J.E., A.D., and J.K. are employed by Daicel Arbor Biosciences, who produced the targeted-capture panel and performed the capture laboratory services for this study.

References

This article includes 73 references
  1. Steele T.E.. The contributions of animal bones from archaeological sites: the past and future of zooarchaeology.. J. Archaeol. Sci. 2015;56:168–176.
    doi: 10.1016/j.jas.2015.02.036google scholar: lookup
  2. Levine M.. Ageing and Sexing Animal Bones from Archaeological Sites. The use of crown height measurements and eruption-wear sequences to age horse teeth. 1982; pp. 223–255.
    doi: 10.30861/9780860541929google scholar: lookup
  3. Toledo González V., Ortega Ojeda F., Fonseca G.M., García-Ruiz C., Pérez-Lloret P.. Analysis of tooth mark patterns on bone remains caused by wolves (Canis lupus) and domestic dogs (Canis lupus familiaris) for taxonomic identification: a scoping review focused on their value as a forensic tool.. Appl. Anim. Behav. Sci. 2021;240:105356.
    doi: 10.1016/j.applanim.2021.105356google scholar: lookup
  4. Taylor W.T.T., Tuvshinjargal T., Bayarsaikhan J.. Reconstructing equine bridles in the Mongolian bronze age.. J. Ethnobiol. 2016;36:554–570.
    doi: 10.2993/0278-0771-36.3.554google scholar: lookup
  5. Taylor W., Fantoni M., Marchina C., Lepetz S., Bayarsaikhan J., Houle J.-L., Pham V., Fitzhugh W.. Horse sacrifice and butchery in bronze age Mongolia.. J. Archaeol. Sci. Rep. 2020;31:102313.
    doi: 10.1016/j.jasrep.2020.102313google scholar: lookup
  6. Wißing C, Rougier H, Baumann C, Comeyne A, Crevecoeur I, Drucker DG, Gaudzinski-Windheuser S, Germonpré M, Gómez-Olivencia A, Krause J, Matthies T, Naito YI, Posth C, Semal P, Street M, Bocherens H. Stable isotopes reveal patterns of diet and mobility in the last Neandertals and first modern humans in Europe.. Sci Rep 2019 Mar 14;9(1):4433.
    doi: 10.1038/s41598-019-41033-3pmc: PMC6418202pubmed: 30872714google scholar: lookup
  7. Harju S., Olson C.V., Hess J., Webb S.L.. Isotopic analysis reveals landscape patterns in the diet of a subsidized predator, the common raven.. Ecol. Solut. Evid. 2021;2:e12100.
    doi: 10.1002/2688-8319.12100google scholar: lookup
  8. Orlando L., Allaby R., Skoglund P., Der Sarkissian C., Stockhammer P.W., Ávila-Arcos M.C., Fu Q., Krause J., Willerslev E., Stone A.C., Warinner C.. Ancient DNA analysis.. Nat. Rev. Methods Primers. 2021;1:14.
    doi: 10.1038/s43586-020-00011-0google scholar: lookup
  9. Ermini L, Der Sarkissian C, Willerslev E, Orlando L. Major transitions in human evolution revisited: a tribute to ancient DNA.. J Hum Evol 2015 Feb;79:4-20.
    doi: 10.1016/j.jhevol.2014.06.015pubmed: 25532800google scholar: lookup
  10. Frantz LAF, Bradley DG, Larson G, Orlando L. Animal domestication in the era of ancient genomics.. Nat Rev Genet 2020 Aug;21(8):449-460.
    doi: 10.1038/s41576-020-0225-0pubmed: 32265525google scholar: lookup
  11. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes.. Nature 2021 Oct;598(7882):634-640.
    doi: 10.1038/s41586-021-04018-9pmc: PMC8550961pubmed: 34671162google scholar: lookup
  12. Frantz LA, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs.. Science 2016 Jun 3;352(6290):1228-31.
    doi: 10.1126/science.aaf3161pubmed: 27257259google scholar: lookup
  13. Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs.. Nature 2022 Jul;607(7918):313-320.
    doi: 10.1038/s41586-022-04824-9pmc: PMC9279150pubmed: 35768506google scholar: lookup
  14. Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M, Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P, Arbogast RM, Arbuckle B, Bӑlӑşescu A, Barnett R, Bartosiewicz L, Baryshnikov G, Bonsall C, Borić D, Boroneanţ A, Bulatović J, Çakirlar C, Carretero JM, Chapman J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitraşcu V, du Plessis L, Edwards CJ, Erek CM, Erim-Özdoğan A, Ervynck A, Fulgione D, Gligor M, Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK, Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A, Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E, McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou A, Pearson MP, Pinhasi R, Radmanović D, Ricaut FX, Richards M, Sabin R, Sarti L, Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasić N, Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD, Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K, Burger J, Evin A, Girdland-Flink L, Larson G. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.. Proc Natl Acad Sci U S A 2019 Aug 27;116(35):17231-17238.
    doi: 10.1073/pnas.1901169116pmc: PMC6717267pubmed: 31405970google scholar: lookup
  15. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, 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 JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, 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 WR, 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 AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.. Cell 2019 May 30;177(6):1419-1435.e31.
    doi: 10.1016/j.cell.2019.03.049pmc: PMC6547883pubmed: 31056281google scholar: lookup
  16. Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys.. Science 2022 Sep 9;377(6611):1172-1180.
    doi: 10.1126/science.abo3503pubmed: 36074859google scholar: lookup
  17. Daly KG, Mattiangeli V, Hare AJ, Davoudi H, Fathi H, Doost SB, Amiri S, Khazaeli R, Decruyenaere D, Nokandeh J, Richter T, Darabi H, Mortensen P, Pantos A, Yeomans L, Bangsgaard P, Mashkour M, Zeder MA, Bradley DG. Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains.. Proc Natl Acad Sci U S A 2021 Jun 22;118(25).
    doi: 10.1073/pnas.2100901118pmc: PMC8237664pubmed: 34099576google scholar: lookup
  18. Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse.. Science 2017 Apr 28;356(6336):442-445.
    doi: 10.1126/science.aam5298pubmed: 28450643google scholar: lookup
  19. Bower MA, McGivney BA, Campana MG, Gu J, Andersson LS, Barrett E, Davis CR, Mikko S, Stock F, Voronkova V, Bradley DG, Fahey AG, Lindgren G, MacHugh DE, Sulimova G, Hill EW. The genetic origin and history of speed in the Thoroughbred racehorse.. Nat Commun 2012 Jan 24;3:643.
    doi: 10.1038/ncomms1644pubmed: 22273681google scholar: lookup
  20. Marklund L, Moller MJ, Sandberg K, Andersson L. A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses.. Mamm Genome 1996 Dec;7(12):895-9.
    doi: 10.1007/s003359900264pubmed: 8995760google scholar: lookup
  21. Liu X, Zhang Y, Liu W, Li Y, Pan J, Pu Y, Han J, Orlando L, Ma Y, Jiang L. A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses.. Curr Biol 2022 Jan 24;32(2):480-487.e6.
    doi: 10.1016/j.cub.2021.11.052pmc: PMC8796118pubmed: 34906355google scholar: lookup
  22. Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Ruttkay M, Trinks A, Ludwig A. Spotted phenotypes in horses lost attractiveness in the Middle Ages.. Sci Rep 2016 Dec 7;6:38548.
    doi: 10.1038/srep38548pmc: PMC5141471pubmed: 27924839google scholar: lookup
  23. Hanghøj K., Orlando L.. Ancient epigenomics. Springer 2018; pp. 75–111.
    doi: 10.1007/13836_2018_18google scholar: lookup
  24. Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.. Genome Res 2014 Mar;24(3):454-66.
    doi: 10.1101/gr.163592.113pmc: PMC3941110pubmed: 24299735google scholar: lookup
  25. Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.. Science 2014 May 2;344(6183):523-7.
    doi: 10.1126/science.1250368pubmed: 24786081google scholar: lookup
  26. Hanghøj K, Renaud G, Albrechtsen A, Orlando L. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.. Gigascience 2019 Apr 1;8(4).
    doi: 10.1093/gigascience/giz025pmc: PMC6474913pubmed: 31004132google scholar: lookup
  27. Seguin-Orlando A, Donat R, Der Sarkissian C, Southon J, Thèves C, Manen C, Tchérémissinoff Y, Crubézy E, Shapiro B, Deleuze JF, Dalén L, Guilaine J, Orlando L. Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.. Curr Biol 2021 Mar 8;31(5):1072-1083.e10.
    doi: 10.1016/j.cub.2020.12.015pubmed: 33434506google scholar: lookup
  28. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo.. Nature 2010 Feb 11;463(7282):757-62.
    doi: 10.1038/nature08835pmc: PMC3951495pubmed: 20148029google scholar: lookup
  29. Gokhman D, Mishol N, de Manuel M, de Juan D, Shuqrun J, Meshorer E, Marques-Bonet T, Rak Y, Carmel L. Reconstructing Denisovan Anatomy Using DNA Methylation Maps.. Cell 2019 Sep 19;179(1):180-192.e10.
    doi: 10.1016/j.cell.2019.08.035pubmed: 31539495google scholar: lookup
  30. Horvath S. DNA methylation age of human tissues and cell types.. Genome Biol 2013;14(10):R115.
    doi: 10.1186/gb-2013-14-10-r115pmc: PMC4015143pubmed: 24138928google scholar: lookup
  31. Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids.. Commun Biol 2021 Dec 17;4(1):1412.
    doi: 10.1038/s42003-021-02935-zpmc: PMC8683477pubmed: 34921240google scholar: lookup
  32. Horvath S, Lu AT, Haghani A, Zoller JA, Li CZ, Lim AR, Brooke RT, Raj K, Serres-Armero A, Dreger DL, Hogan AN, Plassais J, Ostrander EA. DNA methylation clocks for dogs and humans.. Proc Natl Acad Sci U S A 2022 May 24;119(21):e2120887119.
    doi: 10.1073/pnas.2120887119pmc: PMC9173771pubmed: 35580182google scholar: lookup
  33. Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.. Mol Biol Evol 2016 Dec;33(12):3284-3298.
    doi: 10.1093/molbev/msw184pmc: PMC5100044pubmed: 27624717google scholar: lookup
  34. Brusgaard NØ, Dee MW, Dreshaj M, Erven J, van den Hurk Y, Raemaekers D, Çakırlar C. Hunting before herding: A zooarchaeological and stable isotopic study of suids (Sus sp.) at Hardinxveld-Giessendam, the Netherlands (5450-4250 cal BC).. PLoS One 2022;17(2):e0262557.
    doi: 10.1371/journal.pone.0262557pmc: PMC8809594pubmed: 35108285google scholar: lookup
  35. Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci.. Elife 2021 Jul 6;10.
    doi: 10.7554/eLife.64932pmc: PMC8260231pubmed: 34227937google scholar: lookup
  36. Horvath S, Haghani A, Peng S, Hales EN, Zoller JA, Raj K, Larison B, Robeck TR, Petersen JL, Bellone RR, Finno CJ. DNA methylation aging and transcriptomic studies in horses.. Nat Commun 2022 Jan 10;13(1):40.
    doi: 10.1038/s41467-021-27754-ypmc: PMC8748428pubmed: 35013267google scholar: lookup
  37. Song J.. Bias corrections for Random Forest in regression using residual rotation.. J. Korean Stat. Soc. 2015;44:321–326.
    doi: 10.1016/j.jkss.2015.01.003google scholar: lookup
  38. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Bánffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M, Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler SL, Risch R, Rojo Guerra MA, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW, Reich D. Massive migration from the steppe was a source for Indo-European languages in Europe.. Nature 2015 Jun 11;522(7555):207-11.
    doi: 10.1038/nature14317pmc: PMC5048219pubmed: 25731166google scholar: lookup
  39. Fages A., Seguin-Orlando A., Germonpré M., Orlando L.. Horse males became over-represented in archaeological assemblages during the Bronze Age.. J. Archaeol. Sci. Rep. 2020;31:102364.
    doi: 10.1016/j.jasrep.2020.102364google scholar: lookup
  40. Sharp AJ, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, Antonarakis SE. DNA methylation profiles of human active and inactive X chromosomes.. Genome Res 2011 Oct;21(10):1592-600.
    doi: 10.1101/gr.112680.110pmc: PMC3202277pubmed: 21862626google scholar: lookup
  41. Schubert M., Mashkour M., Gaunitz C., Fages A., Seguin-Orlando A., Sheikhi S., Alfarhan A.H., Alquraishi S.A., Al-Rasheid K.A., Chuang R.. Zonkey: a simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages.. J. Archaeol. Sci. 2017;78:147–157.
    doi: 10.1016/j.jas.2016.12.005google scholar: lookup
  42. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis.. BMC Bioinformatics 2008 Dec 29;9:559.
    doi: 10.1186/1471-2105-9-559pmc: PMC2631488pubmed: 19114008google scholar: lookup
  43. Lepetz S.. Horse sacrifice in a Pazyryk culture Kurgan: the princely tomb of Berel'(Kazakhstan). selection Criteria and slaughter procedures.. Anthropozoologica 2013;48:309–321.
    doi: 10.5252/az2013n2a9google scholar: lookup
  44. Chechushkov I.V., Usmanova E.R., Kosintsev P.A.. Early evidence for horse utilization in the Eurasian steppes and the case of the Novoil’inovskiy 2 Cemetery in Kazakhstan.. J. Archaeol. Sci. Rep. 2020;32:102420.
    doi: 10.1016/j.jasrep.2020.102420google scholar: lookup
  45. Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.. Bioinformatics 2013 Jul 1;29(13):1682-4.
    doi: 10.1093/bioinformatics/btt193pmc: PMC3694634pubmed: 23613487google scholar: lookup
  46. Team R.C.. R: a language and environment for statistical computing. 2013.
  47. Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging.. BMC Res Notes 2016 Feb 12;9:88.
    doi: 10.1186/s13104-016-1900-2pmc: PMC4751634pubmed: 26868221google scholar: lookup
  48. Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.. Nat Protoc 2014 May;9(5):1056-82.
    doi: 10.1038/nprot.2014.063pubmed: 24722405google scholar: lookup
  49. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.. Nat Methods 2012 Mar 4;9(4):357-9.
    doi: 10.1038/nmeth.1923pmc: PMC3322381pubmed: 22388286google scholar: lookup
  50. Lepetz S., Clavel B., Alioğlu D., Chauvey L., Schiavinato S., Tonasso-Calvière L., Liu X., Fages A., Khan N., Seguin-Orlando A.. Historical management of equine resources in France from the Iron age to the modern period.. J. Archaeol. Sci. Rep. 2021;40:103250.
    doi: 10.1016/j.jasrep.2021.103250google scholar: lookup
  51. Clavel B., Lepetz S., Chauvey L., Schiavinato S., Tonasso-Calvière L., Liu X., Fages A., Khan N., Seguin-Orlando A., Der Sarkissian C.. Sex in the city: uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France.. J. Archaeol. Sci. Rep. 2022;41:103341.
    doi: 10.1016/j.jasrep.2022.103341google scholar: lookup
  52. Foucras S., Caillat P., Goudemez S., Nuviala P., Balasse M., Cabanis M., Ferret C.. Sépultures de chevaux devant Gergovie, archéozoologie des rituels gaulois.. 2019.
  53. Méniel P., Jouin M.. Les inhumations d’animaux de Vertault (Côte d’Or, début de notre ère). 2000; 2020/10/31 Edition.
    doi: 10.1093/bib/bbaa227google scholar: lookup
  54. Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Bradley DG, Orlando L. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.. Mol Ecol Resour 2016 Mar;16(2):459-69.
    doi: 10.1111/1755-0998.12470pubmed: 26401836google scholar: lookup
  55. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.. Nucleic Acids Res 2010 Apr;38(6):e87.
    doi: 10.1093/nar/gkp1163pmc: PMC2847228pubmed: 20028723google scholar: lookup
  56. Rohland N, Harney E, Mallick S, Nordenfelt S, Reich D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130624.
    doi: 10.1098/rstb.2013.0624pmc: PMC4275898pubmed: 25487342google scholar: lookup
  57. Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski's horses.. Science 2018 Apr 6;360(6384):111-114.
    doi: 10.1126/science.aao3297pubmed: 29472442google scholar: lookup
  58. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing.. Cold Spring Harb Protoc 2010 Jun;2010(6):pdb.prot5448.
    doi: 10.1101/pdb.prot5448pubmed: 20516186google scholar: lookup
  59. Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.. Mol Ecol 2021 Dec;30(23):6144-6161.
    doi: 10.1111/mec.15977pubmed: 33971056google scholar: lookup
  60. Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Improved reference genome for the domestic horse increases assembly contiguity and composition.. Commun Biol 2018;1:197.
    doi: 10.1038/s42003-018-0199-zpmc: PMC6240028pubmed: 30456315google scholar: lookup
  61. Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines.. Sci Rep 2019 Apr 15;9(1):6095.
    doi: 10.1038/s41598-019-42640-wpmc: PMC6465346pubmed: 30988347google scholar: lookup
  62. Poullet M., Orlando L.. Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes.. Front. Ecol. Evol. 2020;8:105.
    doi: 10.3389/fevo.2020.00105google scholar: lookup
  63. Schmidt M, Maixner F, Hotz G, Pap I, Szikossy I, Pálfi G, Zink A, Wagner W. DNA methylation profiling in mummified human remains from the eighteenth-century.. Sci Rep 2021 Jul 29;11(1):15493.
    doi: 10.1038/s41598-021-95021-7pmc: PMC8322318pubmed: 34326450google scholar: lookup
  64. Niiranen L, Leciej D, Edlund H, Bernhardsson C, Fraser M, Quinto FS, Herzig KH, Jakobsson M, Walkowiak J, Thalmann O. Epigenomic Modifications in Modern and Ancient Genomes.. Genes (Basel) 2022 Jan 20;13(2).
    doi: 10.3390/genes13020178pmc: PMC8872240pubmed: 35205223google scholar: lookup
  65. Zhang W, Spector TD, Deloukas P, Bell JT, Engelhardt BE. Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements.. Genome Biol 2015 Jan 24;16(1):14.
    doi: 10.1186/s13059-015-0581-9pmc: PMC4389802pubmed: 25616342google scholar: lookup
  66. Breiman L.. Random forests.. Mach. Learn. 2001;45:5–32.
    doi: 10.1023/A:1010933404324google scholar: lookup
  67. Friedman J, Hastie T, Tibshirani R. Regularization Paths for Generalized Linear Models via Coordinate Descent.. J Stat Softw 2010;33(1):1-22.
    doi: 10.18637/jss.v033.i01pmc: PMC2929880pubmed: 20808728google scholar: lookup
  68. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays.. Bioinformatics 2001 Jun;17(6):520-5.
    doi: 10.1093/bioinformatics/17.6.520pubmed: 11395428google scholar: lookup
  69. Gardner ST, Bertucci EM, Sutton R, Horcher A, Aubrey D, Parrott BB. Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda).. Mol Ecol Resour 2023 Jan;23(1):131-144.
    doi: 10.1101/2022.01.27.477887pubmed: 35957540google scholar: lookup
  70. Horvath S, Raj K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing.. Nat Rev Genet 2018 Jun;19(6):371-384.
    doi: 10.1038/s41576-018-0004-3pubmed: 29643443google scholar: lookup
  71. Raznahan A, Parikshak NN, Chandran V, Blumenthal JD, Clasen LS, Alexander-Bloch AF, Zinn AR, Wangsa D, Wise J, Murphy DGM, Bolton PF, Ried T, Ross J, Giedd JN, Geschwind DH. Sex-chromosome dosage effects on gene expression in humans.. Proc Natl Acad Sci U S A 2018 Jul 10;115(28):7398-7403.
    doi: 10.1073/pnas.1802889115pmc: PMC6048519pubmed: 29946024google scholar: lookup
  72. Dimitriadou E., Hornik K., Leisch F., Meyer D., Weingessel A.. E1071: misc functions of the department of statistics (E1071), TU wien. 2009.
  73. Uddin S, Haque I, Lu H, Moni MA, Gide E. Comparative performance analysis of K-nearest neighbour (KNN) algorithm and its different variants for disease prediction.. Sci Rep 2022 Apr 15;12(1):6256.
    doi: 10.1038/s41598-022-10358-xpmc: PMC9012855pubmed: 35428863google scholar: lookup

Citations

This article has been cited 4 times.
  1. Crubézy É, Guarino-Vignon P, Seguin-Orlando A, Der Sarkissian C, Hanghøj K, Duchesne S, Gérard P, Thèves C, Alcouffe A, Romanova L, Nikolaeva D, Alekseeva L, Hochstrasser-Petit C, Zvénigorosky V, Keyser C, Ludes B, Petit M, Dabernat H, Géraut A, Jyrkov E, Sharaborin A, Kirianov N, Tsydenova N, Dambueva I, Bazarof B, Boland A, Deleuze JF, Bravina R, Alexeev A, Patin É, Stépanoff C, Quintana-Murci L, Orlando L. An ancient DNA perspective on the Russian conquest of Yakutia. Nature 2026 Feb;650(8101):389-398.
    doi: 10.1038/s41586-025-09856-5pubmed: 41501450google scholar: lookup
  2. Sawyer S, Gelabert P, Yakir B, Llanos-Lizcano A, Sperduti A, Bondioli L, Cheronet O, Neugebauer-Maresch C, Teschler-Nicola M, Novak M, Pap I, Szikossy I, Hajdu T, Moiseyev V, Gromov A, Zariņa G, Meshorer E, Carmel L, Pinhasi R. Improved detection of methylation in ancient DNA. Genome Biol 2024 Oct 10;25(1):261.
    doi: 10.1186/s13059-024-03405-5pubmed: 39390557google scholar: lookup
  3. Çokoğlu SS, Koptekin D, Fidan FR, Somel M. Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise. Evol Appl 2024 Jul;17(7):e13743.
    doi: 10.1111/eva.13743pubmed: 38957308google scholar: lookup
  4. Orlando L. A genetic window into the human social past. Proc Natl Acad Sci U S A 2023 Sep 12;120(37):e2312672120.
    doi: 10.1073/pnas.2312672120pubmed: 37647367google scholar: lookup
Subscribe to our newsletter
Join 99,727 horse owners like you who receive our email updates on horse health and nutrition.