From Ancient DNA to Modern Livestock: Paleogenomics

Year : 2023 | Volume : 01 | Issue : 02 | Page : 1-6

    Naveen Kumar Sheoran

  1. M.V.Sc Scholar, Department of Animal Genetics and Breeding, LUVAS, Hisar,, Haryana, India


Paleogenomics, an interdisciplinary blend of paleontology and genomics, has revolutionized our understanding of ancient DNA and its applications across various fields. In Animal Genetics and Breeding, this field has emerged as a pivotal tool providing invaluable insights into the historical genetics of domesticated animals. By reconstructing and analyzing the genomes of long-extinct organisms, paleogenomics sheds light on genetic diversity, evolutionary dynamics, and adaptations of ancient species. Paleogenomics significantly impacts animal breeding by uncovering the genetic heritage of livestock animals like cattle, pigs, sheep, and chickens. The ancient DNA study also contributes to understanding genetic adaptations and disease resistance. By comparing ancient and modern genomes, researchers discern historical genetic changes that conferred resilience and adaptation to specific environments. The knowledge of past genetic variations helps guide selective breeding efforts in present animal populations. It enables the rediscovery of lost genetic variations due to human-driven selection and bottlenecks, helping create breeding and conservation plans that prioritize diversity. Although challenges exist in working with fragmented and degraded ancient DNA, advancements in sequencing technologies and extraction methods provide hope for overcoming these obstacles. Furthermore, the reconstruction of genomes from extinct species holds promise for conservation efforts and may restore genetic diversity. As paleogenomics advances, the potential to refine techniques and extract even older DNA samples promises a deeper understanding of genetic variants and the evolution of the human genome over time.

Keywords: Breeding, Genetics, Livestock, Paleogenomics, DNA

[This article belongs to International Journal of Genetic Modifications and Recombinations(ijgmr)]

How to cite this article: Naveen Kumar Sheoran From Ancient DNA to Modern Livestock: Paleogenomics ijgmr 2023; 01:1-6
How to cite this URL: Naveen Kumar Sheoran From Ancient DNA to Modern Livestock: Paleogenomics ijgmr 2023 {cited 2023 Oct 23};01:1-6. Available from:

Full Text PDF


  1. Heintzman PD, Soares AE, Chang D, et al. Paleogenomics. Reviews in Cell Biology and Molecular Medicine. 2006 Sep 15; 1(3):243-67.
  2. Shapiro B, Hofreiter. M Ancient DNA: Methods and Protocols, Methods in Molecular Biology. Humana Press, Springer. 2012., New York.
  3. Dabney J, Knapp M, Glocke I, et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Natl Acad. Sci. USA. 2013., 110 (39), 15758–15763.
  4. Rohland N, Siedel H, Hofreiter M, A rapid column-based ancient DNA extraction method for increased sample throughput. Ecol. Resour. 2010., 10(4): 677–683.
  5. Campos PF and Gilbert TMP, DNA extraction from keratin and chitin, in Ancient DNA: Methods and Protocols, Methods in Molecular Biology (eds B. Shapiro and M. Hofreiter). Humana Press, Springer. 2012., New York, pp. 43–49.
  6. Gilbert MTP, Wilson AS, Bunce M, et al. Ancient mitochondrial DNA from hair. Biol. 2004., 14(12):R463–R464.
  7. Meyer M, and Kircher M, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protoc. 2010., (6):5448.
  8. Kircher M, Analysis of high throughput ancient DNA sequencing data, in Ancient DNA: Methods and Protocols, Methods in Molecular Biology (eds B. Shapiro and M. Hofreiter). Humana Press, Springer. New York, pp. 197–228.
  9. Schubert M, Ermini L, Der Sarkissian C, et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Protoc. 2014., 9 (5):1056–1082.
  10. Green RE, Malaspinas AS, Krause J, et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell., 134 (3):416–426.
  11. Cahill JA, Green RE, Fulton TL, et al. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLos Genet., 9(3).
  12. Meyer M, Kircher M, Gansauge MT, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science., 338 (6104): 222–226.
  13. Prufer K, Racimo F, Patterson N, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature., 505 (7481):43–49.
  14. Rasmussen M, Anzick SL, Waters MR, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature., 506 (7487):225–229.
  15. Raghavan M, Skoglund P, Graf KE, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature., 505 (7481):87–91.
  16. Ramirez O, Burgos-Paz W, Casas E, et al. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity., 131, 46–52.
  17. Sanchez-Quinto F, Schroeder H, Ramirez O, et al. Genomic affinities of two 7000-year-old Iberian hunter-gatherers. Biol. 2012., 22 (16):1494–1499.
  18. Skoglund P, Malmstrom H, Raghavan M, et al. Origins and genetic legacy of Neolithic farmers and hunter gatherers in Europe. Science., 336 (6080):466–469.
  19. Bos KI, Schuenemann VJ, Golding GB, et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature.,478 (7370):506–510.
  20. Smith O, Clapham A, Rose P, et al. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Rep. 2014., 4, 4003.
  21. Orlando L, Ginolhac A, Zhang G, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. 2013 Jul 4; 499(7456):74-8.
  22. Green RE, Krause J, Briggs AW, et al. A draft sequence of the Neandertal genome. Science., 328 (5979):710–722.
  23. Keller A, Graefen A, Ball M, et al. New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Commun. 2012., 3, 698.
  24. Rasmussen M, Li YR, Lindgreen S, et al. Ancient human genome sequence of an extinct Palaeo- Eskimo. Nature., 463 (7282): 757–762.
  25. Olalde I, Allentoft ME, Sanchez-Quinto F, et al. Derived immune and ancestral pigmentation alleles in a 7000-year-old Mesolithic European. Nature., 507 (7491):225–228.
  26. Pedersen JS, Valen E, Velazquez AM, et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. , 24 (3):454–466.
  27. Gokhman D, Lavi, E, Prufer K, et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science., 344 (6183): 523–527.
  28. Bergström A, Frantz L, Schmidt R, et al. Origins and genetic legacy of prehistoric dogs. 2020 Oct 30; 370(6516):557-64.
  29. Groeneveld LF, Lenstra JA, Eding H, et al. Genetic diversity in farm animals–a review. Animal genetics. 2010 May; 41:6-31.

Regular Issue Open Access Review Article
Volume 01
Issue 02
Received August 26, 2023
Accepted September 18, 2023
Published October 23, 2023