The landscape of Neandertal ancestry in present-day humans

@article{Sankararaman2014TheLO,
  title={The landscape of Neandertal ancestry in present-day humans},
  author={Sriram Sankararaman and Swapan Mallick and Michael Dannemann and Kay Pr{\"u}fer and Janet Kelso and Svante P{\"a}{\"a}bo and Nick J. Patterson and David Reich},
  journal={Nature},
  year={2014},
  volume={507},
  pages={354 - 357}
}
Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer… 
The Genetic Cost of Neanderthal Introgression
TLDR
It is inferred that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis, and the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population.
A high-coverage Neandertal genome from Vindija Cave in Croatia
TLDR
The genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, is sequenced to ~30-fold genomic coverage, allowing 10 to 20% more Ne andertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
Limits of long-term selection against Neandertal introgression
TLDR
It is shown that there has been no long-term genome-wide removal of Neandertal DNA, and that the previous result was due to incorrect assumptions about gene flow between African and non-African populations.
Quantifying the contribution of Neanderthal introgression to the heritability of complex traits
TLDR
This work proposes a framework for using quantification of trait heritability and direction of effect in introgressed regions to understand how Neanderthals were different from modern humans, how selection acted on different traits, and how introgression may have facilitated adaptation to non-African environments.
The phenotypic legacy of admixture between modern humans and Neandertals
TLDR
It is established that archaic admixture influences disease risk in modern humans, hypotheses about the effects of hundreds of Neandertal haplotypes are provided, and the utility of EHR data in evolutionary analyses is demonstrated.
The limits of long-term selection against Neandertal introgression
TLDR
It is found that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.
Multiple episodes of interbreeding between Neanderthals and modern humans
TLDR
A simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations, indicating a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.
Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage
TLDR
This study presents a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and shows that they can be traced back to multiple introgression events, in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.
...
...

References

SHOWING 1-10 OF 44 REFERENCES
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
TLDR
The results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations.
The Date of Interbreeding between Neandertals and Modern Humans
TLDR
The extent of linkage disequilibrium (LD) in the genomes of present-day Europeans is measured and it is found that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000-65,000 year ago.
A Draft Sequence of the Neandertal Genome
TLDR
The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
The complete genome sequence of a Neandertal from the Altai Mountains
TLDR
It is shown that interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene and a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans is established.
An X-linked haplotype of Neandertal origin is present among all non-African populations.
TLDR
Analysis of 6,092 X-chromosomes from all inhabited continents indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.
Neandertal origin of genetic variation at the cluster of OAS immunity genes.
TLDR
DNA sequence variation in the OAS gene cluster on chromosome 12 is surveyed and strong evidence that a haplotype extending for ~185 kb introgressed from Neandertals is provided, consistent with neutral introgression.
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
TLDR
The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
An integrated map of genetic variation from 1,092 human genomes
TLDR
It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites.
Genetic history of an archaic hominin group from Denisova Cave in Siberia
TLDR
A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
...
...