Abstract
Contamination
Archaic Hominins
A DNA, from Modern Humans
Discussion
Note
References
Abstract
We review studies of genomic data obtained by sequencing hominin fossils, with particular emphasis on the unique information that ancient DNA (A DNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, a DNA, has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denison, and has allowed us to disentangle complex selective processes. Information from A DNA, studies is nowhere near saturation, and we believe that future a DNA sequences will continue to change our understanding of hominin history.
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The genomics revolution is well under way. At the time that the first human genomic sequels were obtained (1, 2), it was almost inconceivable that within 15 y thousands of genomes from people around the world would be sequenced, many to a high depth of coverage (3). It was probably even less conceivable that partial or complete genomic sequences would be obtained from hundreds of modern human fossils (4–6), several Neanderthal fossils (7, 8), and even fossils of a previously unknown sister group of Neanderthals, called Denison (9, 10) Fig. Some of these ancient genomes have been sequenced to such high depth that their error rates rival those of high-coverage sequences from present-day human
A human polemic revolution. The maps show the location of human remains that have yielded whole genomes (closed circles) and high-density SNP capture datasets (open circles) of medium and high average coverage (>1×) during the past 6 y. The colors denote the year of publication of each ancient DNA study. Note that some studies cited also include genomes and SNP capture datasets of lower coverage, which are not included in the map. The timeline displays the dating of the remains, on a logarithmic timescale. The references included in this figure but not mentioned in the main text are refs. 69–77.
The wealth of present-day and ancient genomic data has greatly increased what is demanded of population geneticists. When relatively few loci could be studied using marker loci—chiefly blood groups, alloys, and microsatellites—gross descriptive statistics, such as heterozygosity, Wright’s FST, and various genetic distances were sufficient to characterize broad patterns of population differentiation. Application of these classic methods was pioneered by Luca Call and his many collaborators. As early as 1964, Call et al. (11) published a phylogenetic tree of 15 human populations based on a total of 20 alleles at 5 loci, mostly blood groups, for which adequate published data were available. The authors superimposed the tree on a world map to suggest past dispersal routes. Their map is surprisingly consistent with more recent studies based on vastly more data. Only the connection of Maori to Native Americans disagrees with currently accepted theory, that the Maori descended from Polynesians (12).
At present, not only can geneticists elucidate broad patterns of relationship among populations, but they can also provide detailed answers to historical questions of relevance to archeology and paleo anthropology. When, where, and from what source did particular human populations arise? Who admixed with whom, and when did the admixture take place? Are obvious changes in the archaeological record the result of population replacement or cultural innovation? Did past culture leave any genetic descendants? As we will discuss, analysis of ancient DNA (A DNA) has been successful in answering several of these questions, but has also raised new questions in the process. Importantly, a DNA, provides a temporal dimension to genetic studies that would be inaccessible with present-day genomes alone, and only now is the full significance of a DNA being explored.
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