Ancient DNA and Our Humanity
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 of 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. Many even go so far as to name him as the father of evolutionary genetics. Pääbo’s prolific research career has brought him into intimate contact with genomes of all kinds; from ancient Egyptian mummies to Neanderthals to extinct cave bears. In an attempt to provide a brief biography before diving into more complex stories, I will explain some of his major achievements. In the 1980’s, Pääbo troubleshooted the myriad technical issues in 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 Neanderthal, Homo neanderthalensis, the archaic cousin of humanity that went extinct around 30,000 years ago. Initially, Pääbo and his team were limited by poor DNA sequencing technologies so they worked on small projects including characterizing Neanderthal mitochondrial DNA and a few nuclear genes [2]. Eventually, with many collaborators, Pääbo announced that 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 undertake unprecedented comparison and analysis of the two genomes to uncover genetic differences between the two and implications for human evolution in the ~400,000 years since the human lineage split from Neanderthals [4]. In short, Pääbo has and is shaping the field of evolutionary genetics with his innovative research and emerged as the world expert on ancient DNA. Sifting through the scientific literature, you simply don’t find a publication concerning ancient DNA that doesn’t have his name all over the citations.
Essential to Pääbo’s research was the rise of efficient DNA sequencing technologies starting in the late 1980’s. Genetic information is encoded in bases; these bases are Adenine, Cytosine, Guanine, and Thymine (A, C, G, and T). They pair up in DNA — A always with T and C always with G — to encode biological functions. The human genome contains around 3 billion of these base pairs (bp). The way we “read” the order of these bases is called sequencing. The first methods of sequencing, while revolutionary at the time, could only reliably provide ~500bp of reads [5]. To sequence whole genomes, these methods were wildly inefficient and hardly possible. Luckily for researchers, the early 1990’s was a golden age for biotechnologies with rapid advances in many molecular techniques including sequencing. An efficient technique known as High Throughput Sequencing involves attaching fragmented DNA to a chip followed by base addition and detection [6]. Even with the technical power of High Throughput Sequencing (sequences are generated many orders of magnitude faster than previous methods), working with the ancient Neanderthal DNA presented challenges of its own. Pääbo spent not an insignificant portion of his career developing complex protocols to determine reliable and authentic sequences from fragmented ancient DNA. Chief among these difficulties 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. In amplifying DNA, 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 reveals that Neanderthals are significantly more closely related to all non-African humans than to their counterpart populations that never left Africa. The data suggest that 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 that modern Eurasian populations have 1–4% 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 that a small African population of humans migrated, and as they met other archaic hominins, humans drove them to extinction by being more evolutionarily fit. The 1–4% Neanderthal DNA that persists today in non-African genomes brings along genetic relics which have suspected effects in humans. For example, sequences imply that humans acquired Neanderthal versions of genes involved in keratin filament (a protein that makes up hair and fingernails) formation that may have helped early humans adapt to harsher non-African environments [3].
I’d now like to travel a bit further back in evolutionary history and examine the genetic narrative of 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 uncharacterized, at this point it is beyond reasonable doubt that 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 of all, FOXP2 is an unusually conserved gene among mammals [10]. To be “conserved” in a genetic sense means that the sequence of the gene has little change over evolutionary history. 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 that 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 that the gene may have experienced strong positive selecting 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 the mice, the scientists observed 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” that 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].
Perhaps the most endearing part of this story is the fact that this man’s prolific career started as a childhood obsession with ancient Egypt. Constantly reading books about ancient civilizations, Pääbo begged his mother for years to take him to visit Egypt and when he was thirteen, she finally gave in. He held onto this fascination through his education and during his Ph.D., worked to analyze DNA from Egyptian mummies on nights and weekends (his advisor, an Immunology professor, had no knowledge of this). Pääbo’s results were published as the cover article of Nature, kicking off his illustrious career. If anything, Pääbo’s story is a lesson to remain interested as we go through life; if a little boy can hold on to his love of ancient Egypt and translate that into becoming the world expert on ancient DNA and human origins, our future is bright.
References:
1. Pääbo S. 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 S. 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.
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7. Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. 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 L. 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 Biol. 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 O. 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.