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endogamia desinovans

endogamia desinovans

DNA, Ancient CARLES LALUEZA-FOX Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Spain Ancient DNA (aDNA) is the isolation and analysis of DNA sequences from ancient organisms. Since the mid-1980s, it has promoted different scientific fields that benefit from a temporal dimension, including historical anthropology, archaeology, biological evolution, biomedicine, forensics, and paleontology. Within these fields, aDNA can contribute to areas such as phylogeny and systematics, adaptation, genetic diversity, migration, and admixture. The specimens subjected to aDNA research range from rather recent, historical specimens to paleontological samples that are hundreds of thousands of years old. The genetic information varies from a few tens of nucleotides to complete nuclear genomes. The aDNA field officially started in 1984, when Russell Higuchi and collaborators extracted and sequenced DNA fragments from dry tissue from a quagga museum specimen—a kind of South African zebra that became extinct in the nineteenth century (Higuchi et al. 1984). A year later, Svante Pääbo—arguably the leading researcher in the field—retrieved long nuclear DNA sequences (now widely accepted to derive from modern human contaminants) from a 2,500-year-old human Egyptian mummy (Pääbo 1985). These pioneer studies were based on direct sequencing of cloning products, a difficult and laborious approach that could have confined the field to the category of scientific curiosities. However, the advent of the polymerase chain reaction (PCR) technique, which allowed the exponential amplification of specific sequences from minute initial amounts of DNA, boosted the aDNA field for the next two decades. One of the first applications of the PCR was the retrieval of DNA from bones and teeth in 1989, which are far more abundant than mummified tissues. Because there are thousands of mitochondrial DNA (mtDNA) copies per cell, animal aDNA research essentially targeted mtDNA genes for phylogenetic studies (in the case of extinct species) and for population genetic studies (in the case of past human populations). The former included some emblematic species such as mammoths, cave bears, the moa, the Tasmanian wolf, and ground sloths. Early in the 1990s, several extraordinary claims that DNA from specimens millions of years old could be successfully extracted and sequenced were reported in high-profile journals. Among the most remarkable of these were putative sequences from a 17- to 20-million-year-old magnolia leaf from Miocene lake sediments, from insects preserved in amber that were ten to hundreds of million years old, and from dinosaur bones. Eventually, these studies proved to be irreproducible and almost certainly attributable to laboratory artifacts or contamination incidents. As a consequence of these controversial studies, authentication standards to ensure The International Encyclopedia of Anthropology. Edited by Hilary Callan. © 2018 John Wiley & Sons, Ltd. Published 2018 by John Wiley & Sons, Ltd. DOI: 10.1002/9781118924396.wbiea1571 2 DNA, A NCIENT the quality and reproducibility of the ancient DNA sequences were subsequently established. The problem of contamination was already apparent in human samples, in which endogenous DNA can be expected to be indistinguishable from exogenous, modern DNA. Owing to the power of the PCR, a recent intact DNA sequence can outcompete the degraded, endogenous sequences and become the dominant product of the reaction. This is the reason behind the fact that many pioneer aDNA studies on ancient humans focused on continents such as the Americas where European contaminants might hopefully be exposed. Some of them, however, analyzed prehistoric European remains, using stringent precautions such as replication of the results in independent laboratories and cloning of PCR products to unravel potential contaminants and DNA damage. The culmination of the methodological efforts developed during the first ten years of aDNA research was the landmark publication in 1997 of the first Neanderthal DNA sequence (the hypervariable region 1 of the mtDNA from the Feldhofer type specimen) by Pääbo and collaborators (Krings et al. 1997). The data showed no evidence of interbreeding between Neanderthals and modern humans, at least to a level sufficient to result in Neanderthal mtDNA introgression into the modern human mtDNA gene pool. In the fifteen years after the publication other Neanderthal sequences from different sites were retrieved with the same technical approach, confirming the original findings and pointing to a reduced genetic diversity. The discovery of uncontaminated Neanderthal bones, some of them freshly excavated under controlled conditions, for example, those from the El Sidrón site (Spain), allowed the retrieval of specific nuclear genes associated with phenotypic traits. These included the FOXP2 gene, which is related to the orofacial movements involved in language and speech (Neanderthals carried the same variants as modern humans), and the MC1R gene, which plays a role in hair and skin pigmentation (some Neanderthals carried a specific variant that likely resulted in red hair). The advent of the new sequencing technologies After the development of the first so-called second-generation sequencing (SGS) technologies in 2005, it was possible to retrieve first complete Neanderthal mitochondrial genome in 2008 and, later on, partial or complete ancient nuclear genomes. The new technologies allowed precise estimates of modern human contamination in the high-coverage mtDNA genomes obtained. Also, they provided a further evidence of authenticity by describing a specific damage pattern present at the ends of the ancient DNA sequences; the diagnostic misincorporation pattern arises from the deamination of cytosines overhanging fragmented DNA sequences. These developments culminated in the publication in 2010 of the Neanderthal genome draft (at 1.3 depth of coverage), essentially built with data from three bones from the Vindija site in Croatia and directed by Svante Pääbo at the Max Planck Institute in Leipzig. Maybe the most surprising finding of this work was the evidence DNA, A NCIENT 3 that all non-Africans shared around 2.5 percent more derived alleles with Neanderthals than with sub-Saharan Africans, implying that interbreeding took place between both populations about 60,000 to 50,000 years ago, probably in the Near East. In addition, the Neanderthal genome provided a short list of about eighty genes that had derived alleles in the modern human lineage not shared in the Neanderthal lineage. This list, including genes involved in metabolism, skeletal morphology, skin histology, and even cognition, could underlie specific modern human traits and thus should be functionally studied. In 2010 not only was the long-expected Neanderthal genome published but also that of a previously unknown hominin, called Denisovan, named after the cave in the Altai Mountains where the remains of a morphologically undiagnostic finger bone were discovered two years earlier. The sequencing of this bone and subsequent analyses revealed that Denisovans and Neanderthals were sister groups sharing a common ancestor around 450,000 years ago. The divergence time with modern humans was estimated to be around 600,000 years ago. In addition to clarifying the general hominin phylogeny, it was also detected that Melanesians and Australian Aborigines shared an additional approximately 3.5 percent of their DNA with the Denisovan individual, implying yet another interbreeding event in Southeast Asia. Subsequent technical developments, such as the single-stranded DNA library preparation method, helped in the generation of high-coverage (more than thirtyfold coverage) genomes from both Neanderthals (Altai Neanderthal, published in 2013) and Denisovans (the original finger bone, published in 2012). A hint of the nuclear Neanderthal diversity was further achieved with the sequencing of three exomes—the protein-coding portion of the genome—from El Sidrón, Vindija, and Altai, as well as three chromosomes 21, after using a capture approach to enrich for endogenous DNA. The analysis of these data showed that Neanderthals had a remarkably low genetic diversity, attributable to a small long-term effective population size. Their declining demography has favored the accumulation of deleterious alleles in regulatory regions of their genomes. There are also signs of endogamy in the form of homozygous chromosomic tracks—and, at least in the Altai individual, evidence of recent consanguinity. The genotype data of a 37,000- to 42,000-year-old specimen from Pestera cu Oase , in Romania provides a tantalizing evidence of yet another interbreeding event with late Neanderthals. This individual seems to carry 5 percent to 11 percent of Neanderthal genes, which suggests that he had a Neanderthal ancestor four to six generations ago. Modern human paleogenomics Theoretical and empirical data show that DNA is expected to be much better preserved in cold and dry environments such as the Arctic permafrost than in temperate climates. Researchers sought advantageous thermal conditions to sequence the first full genomes from ancient modern humans, including a 4,000-year-old Paleo-Eskimo from Greenland in 2010, the 5,300-year-old Tyrolean Iceman from the Italian Alps in 4 DNA, A NCIENT 2012, and in 2014 a 45,000-year-old modern human from Ust’-Ishim in Siberia and a 36,000-year-old modern human from Kostenki 14 in Russia. However, the potentiality of the SGS technologies also made it possible to obtain ancient genomes from less favorable places such as Continental Europe. The retrieval of complete genomes from the Mesolithic and the Neolithic periods included, in 2014, La Braña (Spain), Loschbour (Luxembourg), Stuttgart (Germany), as well as several more individuals from Sweden and Hungary. These genomes allowed the researchers to start investigating the adaptive challenges brought by the complex transition to agriculture and to unravel fine-scale migration patterns. Interestingly, the genes that seem to be under natural selection in Europeans in the last thousands of years are mainly those associated with skin and iris pigmentation—the Mesolithic hunter-gatherers displayed a remarkable phenotype of blue eyes and dark skin—as well as the previously known lactase persistence variant. The emerging paleogenomic evidence will allow testing of competing archaeological hypotheses regarding all periods and geographical areas of the prehistory of each continent. For instance, a genomic analysis of sixty-nine ancient samples has detected a massive migration from the Eurasian Steppe associated with the Kurgan tradition into Western Europe that has been associated with the dispersal of Indo-European languages. In the Americas, the complete sequencing of the 12,600-year-old Anzick 1 genome, associated with the Clovis culture, illustrated the ancestry of one of the first settlers of the continent. It also stirred an ethics debate with modern Amerindian tribes about their homeland ancestry links. As aDNA research moves closer to recent times, social and cultural controversies with indigenous groups are likely to surface again. Superarchaic ancient DNA Beyond 100,000 years, the possibility of DNA survival and retrieval becomes more and more challenging at temperate latitudes. In 2013 the sequencing of a complete genome from a 700,000-year-old horse bone found in permafrost in Yukon (Alaska) marked an upper limit for aDNA studies in the most favorable environmental conditions. It was soon followed by the sequencing of a mtDNA genome of a circa 400,000-year-old hominin from the Sima de los Huesos in Atapuerca (Spain). Interestingly, the skeletal remains had been previously classified as Homo heidelbergensis and have been interpreted as showing some Neanderthal-specific traits, and, yet, the Sima de los Huesos mtDNA forms a clade with the posterior Denisovan individual and not with the Neanderthals. The retrieval of nuclear data suggests that these hominins are in fact related to the Neanderthal lineage. This raises questions about the complex population affinities of hominins from the Middle Pleistocene across Eurasia. This study opens new temporal possibilities for paleogenomic research, although it remains to be seen how many specimens of similar age still preserve DNA. DNA, A NCIENT 5 Future directions of aDNA research In the next years, aDNA research will be able to generate hundreds—if not thousands— of ancient modern human genomes, especially outside the tropics. Although so far almost no paleogenomic data is available from Africa, a critical continent for unraveling human origins, or from the Near East, a crucial area for understanding human dispersals in the Upper Paleolithic and the Neolithic, new methodological and computational developments will likely fill this gap in the future. Researchers will also try to go back in time, although no computational method would be able to identify specific DNA sequences beyond a certain level of fragmentation. Therefore, there are technical as well as bioinformatic limits for DNA retrieval; a reasonable time limit for the aDNA field would be about 1 million years, with a strong dependence on the taphonomic conditions.The reduction in costs of sequencing technologies will lead to a democratization of the field and the growing amount of data will continue revolutionizing the study of the human past for the next decade. SEE ALSO: Archaeological Approaches in Anthropology; Bioarchaeology; Biological and Evolutionary Anthropology; Demography, Prehistoric Human; Genetics, Evolutionary; Genetics of Modern Human Origins and Diversity; Homo: Evolution of the Genus; Hunter-Gatherer Models in Human Evolution; Kinship (Early Human), the Archaeological Evidence for; Migration History; Neanderthals, Biosocial Models of; Speciation in Biology and the Fossil Record REFERENCES AND FURTHER READING Cooper, Alan, and Hendrik N. Poinar. 2000. “Ancient DNA: Do it Right or Not at All.” Science 289: 1139. Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. 2010. “A Draft Sequence of the Neandertal Genome.” Science 328: 710–22. Hagelberg, Erika, Bryan Sykes, and Robert Hedges. 1989. “Ancient Bone DNA Amplified.” Nature 342: 485. Higuchi, Russell, Barbara Bowman, Mary Freiberger, Oliver A. Ryder, and Allan C.Wilson. 1984. “DNA Sequences from the Quagga, an Extinct Member of the Horse Family.” Nature 312: 282–84. Hofreiter, Michael, David Serre, Hendrik N. Poinar, Melanie Kuch, and Svante Pääbo. 2001. “Ancient DNA.” Nature Reviews: Genetics 2: 353–59. Iosif, Lazaridis, Nick Patterson, Alissa Mittnik, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber et al. 2014. “Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans.” Nature 513: 409–13. Krings, Matthias, Anne Stone, Ralf W. Schmitz, Heike Krainitzki, Mark Stoneking, and Svante Pääbo. 1997. “Neandertal DNA Sequences and the Origin of Modern Humans.” Cell 90: 19–30. Olalde, Iñigo, Morten E. Allentoft, Federico Sánchez-Quinto, Gabriel Santpere, Charleston W. K. Chiang, Michael DeGiorgio, Javier Prado-Martinez et al. 2014. “Derived Immune and Ancestral Pigmentation Alleles in a 7,000-year-old Mesolithic European.” Nature 507: 225–28. 6 DNA, A NCIENT Pääbo, S. 1985. “Molecular Cloning of Ancient Egyptian Mummy DNA.” Nature 314: 644–45. Pääbo, S. 2014. Neanderthal Man: In Search of Lost Genomes. Philadelphia: Basic Books. Prüfer, Kay, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze et al. 2014. “The Complete Genome Sequence of a Neanderthal from the Altai Mountains.” Nature 505: 43–49. Rasmussen, Morten, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu et al. 2010. “Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo.” Nature 463: 757–62. Reich, David, Richard E. Green, Martin Kircher, Johannes Krause, Nick Patterson, Eric Y. Durand, Bence Viola et al. 2010. “Genetic History of an Archaic Hominin Group from Denisova Cave in Siberia.” Nature 468: 1053–60.