Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, "ancient DNA" (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches.  Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.

Part1. Concepts, Technical Advances and Challenges

Chapter1. Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA
Chapter2. Paleoproteomics: An Introduction to the Analysis of Ancient Proteins by Soft Ionization Mass Spectrometry
Chapter3. Ancient RNA
Chapter4. Ancient Epigenomics
Part2.
Chapter5. Ancient Pathogens Through Human History: A Paleogenomic Perspective
Chapter6. Paleovirology: Viral Sequences from Historical and Ancient DNA
Chapter7. Reconstructing Past Vegetation Communities Using Ancient DNA from Lake Sediments
Chapter8. Archaeogenomics and Crop Adaptation
Chapter9. Herbarium Genomics: Plant Archival DNA Explored
Chapter10. Paleogenomics of Animal Domestication
Chapter11. Paleogenomic Inferences of Dog Domestication
Chapter12. Of Cats and Men: Ancient DNA Reveals How the Cat Conquered the Ancient World
Chapter13. An Ancient DNA Perspective on Horse Evolution
Chapter14. Primate Paleogenomics
Chapter15. Structural Variants in Ancient Genomes
Chapter16. Genomics of Extinction.