Ancient Human DNA: Phylogenetic Applications
Michael Knapp, Bangor University, Bangor, UK
Michael Hofreiter, University of Potsdam, Potsdam, Germany
Published online: May 2014
Ever since deoxyribonucleic acid (DNA) was first extracted from the remains of long‐dead organisms in the 1980s, researchers have been interested in the investigation
of ancient human DNA. Such studies of DNA extracted from ancient human remains attempt to shed light on the genetic makeup
of archaic and extinct, anatomically modern human populations, as well as on the relationships between these individuals and
modern humans. These studies have long been limited by several factors, including the contamination of ancient samples with
modern human DNA, and the limited accessibility of nuclear DNA from ancient human remains. However, recent innovations in
DNA sequencing technology have lead to a dramatic increase in DNA sequence data available from archaic or extinct human populations
and to unexpected new insights into human evolution.
The study of ancient human DNA is complicated by potential contamination with modern human DNA.
Studies on ancient human DNA have long been limited by the availability of suitable DNA sequencing technologies.
The development of new high‐throughput sequencing technologies has revolutionised the study of ancient human DNA.
The latest genetic analyses of human evolution have provided increasingly more detailed insights into the origin and development
of our own species.
Genetic data now also allow for the study of coevolution of humans and their pathogens.
Keywords: evolution; migration; Neanderthals; Denisovans; ancient DNA; human populations
Bos KI, Schuenemann VJ, Golding GB et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478: 506–510.
Burger J, Kirchner M, Bramanti B, Haak W and Thomas MG (2007) Absence of the lactase‐persistence‐associated allele in early Neolithic Europeans. Proceedings of the National Academy of Sciences of the USA 104: 3736–3741.
Gilbert MTP, Kivisild T, Grønnow B et al. (2008) Paleo‐Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320: 1787–1789.
Green RE, Krause J, Briggs AW et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.
Haak W, Forster P, Bramanti B et al. (2005) Ancient DNA from the first European farmers in 7500‐year‐old Neolithic sites. Science 310: 1016–1018.
Knapp M (2011) The next generation of genetic investigations into the Black Death. Proceedings of the National Academy of Sciences of the USA 108: 15669–15670.
Knapp M and Hofreiter M (2010) Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes 1: 227–243.
Kolman CJ and Tuross N (2000) Ancient DNA analysis of human populations. American Journal of Physical Anthropology 111: 5–23.
Krause J, Fu Q, Good JM et al. (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464: 894–897.
Meyer M, Fu Q, Aximu‐Petri A et al. (2014) A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505: 403–406.
Meyer M, Kircher M, Gansauge M‐T et al. (2012) A high‐coverage genome sequence from an archaic Denisovan individual. Science 338: 222–226.
Pääbo S, Poinar H, Serre D et al. (2004) Genetic analyses from ancient DNA. Annual Review of Genetics 38: 645–679.
Prüfer K, Racimo F, Patterson N et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49.
Rasmussen M, Li Y, Lindgreen S et al. (2010) Ancient human genome sequence of an extinct Palaeo‐Eskimo. Nature 463: 757–762.
Sawyer S, Krause J, Guschanski K, Savolainen V and Pääbo S (2012) Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One 7: e34131.
Shapiro B and Hofreiter M (2014) A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343. DOI: 10.1126/science.1236573.
Bollongino R, Nehlich O, Richards MP et al. (2013) 2000 years of parallel societies in Stone Age Central Europe. Science 342: 479–481.
Rohland N and Hofreiter M (2007) Ancient DNA extraction from bones and teeth. Nature Protocols 2: 1756–1762.
Schuenemann VJ, Singh P, Mendum TA et al. (2013) Genome‐wide comparison of medieval and modern Mycobacterium leprae
. Science 341: 179–183.
Stoneking M and Krause J (2011) Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 12: 603–614.