Ancient DNA

As part of the International Steenbock Lecture Series, the University of Wisconsin-Madison hosted world renowned researcher Svante Pääbo (sv-AH-nte p-AY-b-oh) in December 2016. To place Pääbo into an academic niche proves difficult — he is a world leader in the fields of anthropology, genetics, evolution and molecular biology,  with many even going so far as to name him the ‘father of evolutionary genetics.’ Pääbo’s prolific research career has brought him into intimate contact with genomes of all kinds, ranging from ancient Egyptian mummies to Neanderthals to extinct cave bears. In the 1980s, Pääbo overcame various technical issues related to isolating and characterizing deoxyribonucleic acid (DNA) from Ancient Egyptian Mummies [1]. Over the next decade or so, he became an expert in analyzing ancient DNA. Years later, Pääbo moved on to the archaic cousin of humanity that went extinct around 30,000 years ago: The Neanderthal, or Homo neanderthalensis. Initially, Pääbo and his team were limited by poor DNA sequencing technologies, so they worked on smaller parts of the genome, such as the mitochondrial DNA and a few nuclear genes of Neanderthals [2]. Eventually, with the help of his collaborators, Pääbo announced he and his team had put together a draft sequence of the entire Neanderthal genome in 2010 [3]. This was the crown jewel for Pääbo. With the completion of the Human Genome Project in 2001, he and his colleagues could begin an unprecedented comparison and analysis of the two genomes to uncover genetic differences between the two and implications for human evolution in the approximate 400,000 years since the human lineage split from Neanderthals [4]. In short, Pääbo has shaped and continues to shape the field of evolutionary genetics with his innovative research and has emerged as the world expert on ancient DNA. Sifting through the scientific literature, it’s difficult to find a publication concerning ancient DNA that doesn’t have his name all over the citations.

The rise of efficient DNA sequencing technologies starting in the late 1980s is essential to Pääbo’s research. The human genome contains around three billion base pairs (bp). The way we “read” the order of these bases is called sequencing. Prior to the 1980s, scientists were handicapped by their ability to only reliably sequence around 500bp at a time [5]. Sequencing whole genomes was impossible due to the low throughput nature of the technology. Luckily for researchers, the early 1990s was a golden age for biotechnology with rapid advances in many molecular techniques, including sequencing. One of the most pertinent advances of this golden age was high-throughput sequencing, which allowed for the generation of DNA sequences at a rate magnitudes faster than previous methods [6]. But, even with the new technologies, working with the ancient Neanderthal DNA presented challenges of its own. Pääbo spent a significant portion of his career developing complex protocols to determine reliable and authentic sequences from fragmented ancient DNA. A complication contributing to the amount of time he spent refining his protocols was the issue of contaminant DNA. The same properties of DNA that allow it to persist in archeological specimens for tens of thousands of years give other pieces of contaminating DNA extraordinary longevity as well. When amplifying DNA in the process of sequencing it, a single piece of contaminating DNA can render the results useless [1]. A combination of new technologies, Pääbo’s decades of experience with ancient DNA, and a rational approach allowed his team to announce the draft assembly and analysis of the full Neanderthal genome in the May 2010 issue of the journal Science [3].

While the complete Neanderthal genome does reveal important information on the nature of Homo neanderthalensis, more significant findings appear from analyzing the Neanderthal genome in the context of human genetics. Detailed sequence comparisons between the two hominins provide an unprecedented level of detail on human evolution in the last few hundred thousand years. Put simply, by comparing the modern human to a hominin that we diverged from some time ago, Pääbo’s team identified versions of traits and genes novel to the human genome that may have had functional ramifications. Perhaps the most exciting result from this monumental project was the conclusion that early humans most likely interbred with Neanderthals. Analysis of the frequency of single nucleotide polymorphisms — mutations in one base pair of DNA, known as SNPs — between the Neanderthal and Human genomes revealed Neanderthals are significantly more closely related to all non-African humans than to their counterpart populations that never left Africa. This data suggests Neanderthals exchanged genetic information with early humans that left Africa. Previously, experts made arguments for and against human-Neanderthal interbreeding, both based on poor evidence [7,8]. Pääbo’s molecular findings suggest with strong data-driven evidence, modern Eurasian populations have 1 to 4% Neanderthal DNA due to gene transfer between populations of early humans and Neanderthals. This revelation fundamentally changes our understanding of early human population expansion. Previous models claim a small African population of humans migrated and drove other archaic hominins to extinction by virtue of being more evolutionarily fit. The 1 to 4% Neanderthal DNA that persists today in non-African genomes brings along genetic relics that have suspected effects in humans. For example, sequences imply that humans acquired Neanderthal versions of genes involved in keratin filament formation — a protein that makes up hair and fingernails — may have helped early humans adapt to harsher non-African environments [3].

In light of Pääbo’s work on the Neanderthal genome, there are many genes worthy of further examination. One particularly intriguing gene is Forkhead Box Protein P2 (FOXP2), one of the only human genes known to be essential in the normal development of speech and language. Mutation or inactivation of this gene in humans causes severe disorders in language development [9]. Functional language is something uniquely human and constitutes a symphony of complex anatomical, physiological, neurological and genetic pathways. And while many of the exact functions of FOXP2 are not yet characterized, at this point, it is beyond reasonable doubt this gene plays a role in speech and language development. Now, to dig into the molecular basis behind this claim, we need to examine the evolutionary genetics of the gene. First, FOXP2 is an unusually conserved gene among mammals [10]. To be “conserved” in a genetic sense means the sequence of the gene is observed to be very similar across species over evolutionary. Conserved sequences like this tend to remain conserved unless a scenario where a mutation is favored by selection arises. Two mutations in FOXP2 became fixed in the time following the human lineage’s split from the chimpanzee. We know these mutations arose before many archaic hominins diverged from their common ancestor with humans because Neanderthals share the modern variant of FOXP2 almost identically with humans [11]. These two changes represent a significant increase in the rate of mutation at the FOXP2 locus, indicating the gene may have experienced a strong positive when selected in early hominin populations, possibly indicating that developing speech was an evolutionary boon to early humans [12]. In an effort to characterize the neurological implications of the human FOXP2, Pääbo and his colleagues introduced the human version of FOXP2 into the genomes of mice and observed the phenotypic manifestations of this change. Through complex behavioral assays performed on mice, scientists observed the addition of the gene resulted in a tendency to rely on procedural learning more than the wild type mice. Procedural learning involves the “how” of solving problems and constructs complex neural circuits that provide long term, automatic responses to tasks. While the results of this study are far from conclusive on the role of humanized FOXP2 in mouse learning, one scenario they may suggest is that the human FOXP2 increased the efficiency of human procedural learning which allowed better language acquisition [13]. Whether or not FOXP2 is the “speech gene” many scientists hope it is, it is still a proof of concept in how evolutionary genetics and Pääbo’s research can provide insights into the mechanisms of selection that acted upon archaic hominins and produced the complex, intelligent and industrious species that dominates the earth today: Homo sapiens sapiens [14].


  1. Pääbo Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci U S A. 1989;86(6):1939-43. PubMed PMID: 2928314; PubMed Central PMCID: PMCPMC286820.
  2. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo Neandertal DNA sequences and the origin of modern humans. Cell. 1997;90(1):19-30. PubMed PMID: 9230299
  3. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A draft sequence of the Neandertal genome. Science. 2010;328(5979):710-22. doi: 10.1126/science.1188021. PubMed PMID: 20448178; PubMed Central PMCID: PMCPMC5100745.
  4. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921. doi: 10.1038/35057062. PubMed PMID: 11237011.
  5. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74(12):5463-7. PubMed PMID: 271968; PubMed Central PMCID: PMCPMC431765.
  6. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53-9. doi: 10.1038/nature07517. PubMed PMID: 18987734; PubMed Central PMCID: PMCPMC2581791.
  7. Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proc Natl Acad Sci U S A. 2006;103(48):18178-83. Epub 2006/11/07. doi: 10.1073/pnas.0606966103. PubMed PMID: 17090677; PubMed Central PMCID: PMCPMC1635020.
  8. Currat M, Excoffier Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe. PLOS Biology. 2004;2(12):e421. doi: 10.1371/journal.pbio.0020421.
  9. Lai CS, Fisher SE, Hurst JA, Vargha-Khadem F, Monaco AP. A forkhead-domain gene is mutated in a severe speech and language disorder. Nature. 2001;413(6855):519-23. doi: 10.1038/35097076. PubMed PMID: 11586359.
  10. Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature. 2002;418(6900):869-72. Epub 2002/08/14. doi: 10.1038/nature01025. PubMed PMID: 12192408.
  11. Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, et al. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr 2007;17(21):1908-12 Epub 2007/10/18. doi: 10.1016/j.cub.2007.10.008. PubMed PMID: 17949978.
  12. Zhang J, Webb DM, Podlaha Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics. 2002;162(4):1825-35. PubMed PMID: 12524352; PubMed Central PMCID: PMCPMC1462353.
  13. Schreiweis C, Bornschein U, Burguière E, Kerimoglu C, Schreiter S, Dannemann M, et al. Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. Proc Natl Acad Sci U S A. 2014;111(39):14253-8. Epub 2014/09/15. doi: 10.1073/pnas.1414542111. PubMed PMID: 25225386; PubMed Central PMCID: PMCPMC4191787.
  14. Pääbo S. The human condition-a molecular approach. Cell. 2014;157(1):216-26. doi: 10.1016/j.cell.2013.12.036. PubMed PMID: 24679537.

This piece was featured in Volume II Issue II of JUST. Click here to read more of this issue.