Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture (original) (raw)
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Human Biology, 2011
Ten years after the first draft versions of the human genome were announced, technical progress in both DNA sequencing and ancient DNA analyses has allowed a research team around Ed Green and Svante Pa¨a¨bo to complete this task from infinitely more difficult hominid samples: a few pieces of bone originating from our closest, albeit extinct, relatives, the Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating environmental DNA impregnating the bones and at the same time avoiding the problems of contamination with modern human DNA is in itself a remarkable accomplishment. However, the crucial question in the long run is, what can we learn from such genomic data about hominid evolution?
Tracing the origin of our species through palaeogenomics
BIO Web of Conferences, 2015
The recent breathtaking progress in whole genome sequencing technology allows access to the genomes both of ancient organisms and populations, including those now extinct. Despite the heavy degradation and the extremely low quantities of ancient DNA, it is sometimes possible to sequence an entire genome from a fossil. This enterprise has been successful in the case of fossilized remains from Neanderthals, a lineage of hominids that lived in Europe for 200,000 years and disappeared 30,000 years ago. An even greater surprise was the genome that has been obtained from a small finger bone preserved in a cave in the Siberian Altai Mountains. This genome revealed the existence of a human lineage previously unknown from the fossil record. The corresponding population mixed with the Neanderthals and the ancestors of the present day populations of SouthEast Asia. These hybridization events left different traces in the non-African human populations emphasizing the fact that we are genomic mosaics. The comparison of the different genomes also gives hints to how the genome of present-day populations was shaped and helps us to better understand which parts of our genetic make-up are responsible for the biological features of H. sapiens.
Insights into human genetic variation and population history from 929 diverse genomes
2019
Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits t...
Sequence variations in the public human genome data reflect a bottlenecked population history
Proceedings of the …, 2003
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.
A high-coverage genome sequence from an archaic denisovan individual
2012
We present a DNA library preparation method that has allowed us to reconstruct a high coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.